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Baratsas SG, Niziolek AM, Onel O, Matthews LR, Floudas CA, Hallermann DR, Sorescu SM, Pistikopoulos EN. A framework to predict the price of energy for the end-users with applications to monetary and energy policies. Nat Commun 2021; 12:18. [PMID: 33398000 PMCID: PMC7782726 DOI: 10.1038/s41467-020-20203-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 11/09/2020] [Indexed: 11/21/2022] Open
Abstract
Energy affects every single individual and entity in the world. Therefore, it is crucial to precisely quantify the “price of energy” and study how it evolves through time, through major political and social events, and through changes in energy and monetary policies. Here, we develop a predictive framework, an index to calculate the average price of energy in the United States. The complex energy landscape is thoroughly analysed to accurately determine the two key factors of this framework: the total demand of the energy products directed to the end-use sectors, and the corresponding price of each product. A rolling horizon predictive methodology is introduced to estimate future energy demands, with excellent predictive capability, shown over a period of 174 months. The effectiveness of the framework is demonstrated by addressing two policy questions of significant public interest. Global energy transformation requires quantifying the "price of energy" and studying its evolution. Here the authors present a predictive framework that calculates the average US price of energy, estimating future energy demands for up to four years with excellent accuracy, designing and optimizing energy and monetary policies.
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Affiliation(s)
- Stefanos G Baratsas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA
| | - Alexander M Niziolek
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA
| | - Onur Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA
| | - Logan R Matthews
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA
| | - Detlef R Hallermann
- Department of Finance, Mays Business School, Texas A&M University, College Station, TX, 77843, USA
| | - Sorin M Sorescu
- Department of Finance, Mays Business School, Texas A&M University, College Station, TX, 77843, USA
| | - Efstratios N Pistikopoulos
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, 77843, USA. .,Texas A&M Energy Institute, Texas A&M University, College Station, TX, 77843, USA.
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2
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Demirhan CD, Boukouvala F, Kim K, Song H, Tso WW, Floudas CA, Pistikopoulos EN. An integrated data-driven modeling & global optimization approach for multi-period nonlinear production planning problems. Comput Chem Eng 2020. [DOI: 10.1016/j.compchemeng.2020.107007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Matthews LR, Niziolek AM, Onel O, Pinnaduwage N, Floudas CA. Correction to “Biomass to Liquid Transportation Fuels via Biological and Thermochemical Conversion: Process Synthesis and Global Optimization Strategies”. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b04523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Logan R. Matthews
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
| | - Alexander M. Niziolek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
| | - Onur Onel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
| | - Neesha Pinnaduwage
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
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Abstract
The (global) optimization of energy systems, commonly characterized by high-fidelity and large-scale complex models, poses a formidable challenge partially due to the high noise and/or computational expense associated with the calculation of derivatives. This complexity is further amplified in the presence of multiple conflicting objectives, for which the goal is to generate trade-off compromise solutions, commonly known as Pareto-optimal solutions. We have previously introduced the p-ARGONAUT system, parallel AlgoRithms for Global Optimization of coNstrAined grey-box compUTational problems, which is designed to optimize general constrained single objective grey-box problems by postulating accurate and tractable surrogate formulations for all unknown equations in a computationally efficient manner. In this work, we extend p-ARGONAUT towards multi-objective optimization problems and test the performance of the framework, both in terms of accuracy and consistency, under many equality constraints. Computational results are reported for a number of benchmark multi-objective problems and a case study of an energy market design problem for a commercial building, while the performance of the framework is compared with other derivative-free optimization solvers.
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Affiliation(s)
- Burcu Beykal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Fani Boukouvala
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christodoulos A. Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Efstratios N. Pistikopoulos
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
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Tso WW, Niziolek AM, Onel O, Demirhan CD, Floudas CA, Pistikopoulos EN. Reprint of: Enhancing natural gas-to-liquids (GTL) processes through chemical looping for syngas production: Process synthesis and global optimization. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Onel M, Kieslich CA, Guzman YA, Floudas CA, Pistikopoulos EN. Reprint of: Big data approach to batch process monitoring: Simultaneous fault detection and diagnosis using nonlinear support vector machine-based feature selection. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Matthews LR, Guzman YA, Onel O, Niziolek AM, Floudas CA. Natural Gas to Liquid Transportation Fuels under Uncertainty Using Robust Optimization. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b01638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Logan R. Matthews
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843, United States
| | - Yannis A. Guzman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843, United States
| | - Onur Onel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843, United States
| | - Alexander M. Niziolek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843, United States
| | - Christodoulos A. Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843, United States
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Guzman YA, Sakellari D, Papadimitriou K, Floudas CA. High-throughput proteomic analysis of candidate biomarker changes in gingival crevicular fluid after treatment of chronic periodontitis. J Periodontal Res 2018; 53:853-860. [PMID: 29900535 DOI: 10.1111/jre.12575] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Untargeted, high-throughput proteomics methodologies have great potential to aid in identifying biomarkers for the diagnosis of periodontal disease. The application of such methods to the discovery of candidate biomarkers for the resolution of periodontal inflammation after periodontal therapy has been investigated. MATERIAL AND METHODS Gingival crevicular fluid samples were collected from 10 patients diagnosed with chronic periodontitis at baseline and 1, 5, 9 and 13 weeks after completion of mechanical periodontal treatment. Clinical indices of periodontal disease, including probing depth, recession, clinical attachment level and bleeding on probing, were recorded at baseline and 13 weeks. Samples were analyzed using an online liquid chromatography-nanoelectrospray-hybrid ion trap-Orbitrap mass spectrometer. Spectra were processed with the PILOT_PROTEIN proteomics software suite. RESULTS Clinical parameters were significantly improved 13 weeks after treatment (Wilcoxon signed ranks test, P < .05). From the substantial number of identified proteins, a small subset was extracted by filter methods that included temporal pattern matching, logistic function fitting and mixed-integer linear optimization. This subset includes azurocidin, lysozyme C and myosin-9 as candidate biomarkers prominent at baseline and alpha-smooth muscle actin as prominent 13 weeks after treatment. Cross-validation studies yielded average predictive accuracy and area under the curve of 0.900 and 0.930, respectively. CONCLUSION High-throughput proteomic analysis can contribute to identifying endpoints of periodontal therapy. These candidate biomarkers should be evaluated for clinical efficacy.
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Affiliation(s)
- Y A Guzman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, USA
| | - D Sakellari
- Department of Preventive Dentistry, Periodontology and Implant Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - K Papadimitriou
- Department of Preventive Dentistry, Periodontology and Implant Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - C A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, USA
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Tso WW, Niziolek AM, Onel O, Demirhan CD, Floudas CA, Pistikopoulos EN. Enhancing natural gas-to-liquids (GTL) processes through chemical looping for syngas production: Process synthesis and global optimization. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Mitsos A, Asprion N, Floudas CA, Bortz M, Baldea M, Bonvin D, Caspari A, Schäfer P. Challenges in process optimization for new feedstocks and energy sources. Comput Chem Eng 2018. [DOI: 10.1016/j.compchemeng.2018.03.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Onel M, Kieslich CA, Guzman YA, Floudas CA, Pistikopoulos EN. Big Data Approach to Batch Process Monitoring: Simultaneous Fault Detection and Diagnosis Using Nonlinear Support Vector Machine-based Feature Selection. Comput Chem Eng 2018; 115:46-63. [PMID: 30386002 DOI: 10.1016/j.compchemeng.2018.03.025] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This paper presents a novel data-driven framework for process monitoring in batch processes, a critical task in industry to attain a safe operability and minimize loss of productivity and profit. We exploit high dimensional process data with nonlinear Support Vector Machine-based feature selection algorithm, where we aim to retrieve the most informative process measurements for accurate and simultaneous fault detection and diagnosis. The proposed framework is applied to an extensive benchmark dataset which includes process data describing 22,200 batches with 15 faults. We train fault and time-specific models on the prealigned batch data trajectories via three distinct time horizon approaches: one-step rolling, two-step rolling, and evolving which varies the amount of data incorporation during modeling. The results show that two-step rolling and evolving time horizon approaches perform superior to the other. Regardless of the approach, proposed framework provides a promising decision support tool for online simultaneous fault detection and diagnosis for batch processes.
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Affiliation(s)
- Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Chris A Kieslich
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA.,Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Yannis A Guzman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.,Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Efstratios N Pistikopoulos
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.,Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
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Onel O, Niziolek AM, Butcher H, Wilhite BA, Floudas CA. Multi-scale approaches for gas-to-liquids process intensification: CFD modeling, process synthesis, and global optimization. Comput Chem Eng 2017. [DOI: 10.1016/j.compchemeng.2017.01.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Niziolek AM, Onel O, Floudas CA. Municipal solid waste to liquid transportation fuels, olefins, and aromatics: Process synthesis and deterministic global optimization. Comput Chem Eng 2017. [DOI: 10.1016/j.compchemeng.2016.07.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Khoury GA, Smadbeck J, Kieslich CA, Koskosidis AJ, Guzman YA, Tamamis P, Floudas CA. Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double-blind predictions during the CASP11 experiment. Proteins 2017; 85:1078-1098. [PMID: 28241391 DOI: 10.1002/prot.25274] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 02/01/2017] [Accepted: 02/14/2017] [Indexed: 12/28/2022]
Abstract
Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794-814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7-10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics-based and hybrid energy functions, as well as a coordinate-free representation of the protein structure through distance-binning Cα-Cα distances to capture fine-grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross-validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7-10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web-servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/. Proteins 2017; 85:1078-1098. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- George A Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Chris A Kieslich
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas
| | - Alexandra J Koskosidis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas
| | - Yannis A Guzman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey.,Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas
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Liu T, First EL, Hasan MF, Floudas CA. Corrigendum to “A multi-scale approach for the discovery of zeolites for hydrogen sulfide removal” [Comput. Chem. Eng. (2016)]. Comput Chem Eng 2016. [DOI: 10.1016/j.compchemeng.2016.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Zhang BJ, Chen QL, Li J, Floudas CA. Operational strategy and planning for raw natural gas refining complexes: Process modeling and global optimization. AIChE J 2016. [DOI: 10.1002/aic.15416] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bing J. Zhang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Petrochemical Energy Conservation, Key Lab of Low-carbon Chemistry & Energy Conservation of Guangdong Province; Sun Yat-Sen University; No. 135, Xingang West Road Guangzhou 510275 China
| | - Qing L. Chen
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Petrochemical Energy Conservation, Key Lab of Low-carbon Chemistry & Energy Conservation of Guangdong Province; Sun Yat-Sen University; No. 135, Xingang West Road Guangzhou 510275 China
| | - Jie Li
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; 3122 TAMU College Station TX 77843
- Texas A&M Energy Institute, Texas A&M University; 3372 TAMU College Station TX 77843
| | - Christodoulos A. Floudas
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; 3122 TAMU College Station TX 77843
- Texas A&M Energy Institute, Texas A&M University; 3372 TAMU College Station TX 77843
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Li J, Xiao X, Boukouvala F, Floudas CA, Zhao B, Du G, Su X, Liu H. Data‐driven mathematical modeling and global optimization framework for entire petrochemical planning operations. AIChE J 2016. [DOI: 10.1002/aic.15220] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jie Li
- Institute of Process Engineering, Chinese Academy of SciencesBeijing100190 P. R. China
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843
- Texas A&M Energy Institute, Texas A&M UniversityCollege Station TX77843
| | - Xin Xiao
- Institute of Process Engineering, Chinese Academy of SciencesBeijing100190 P. R. China
| | - Fani Boukouvala
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843
- Texas A&M Energy Institute, Texas A&M UniversityCollege Station TX77843
| | - Christodoulos A. Floudas
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843
- Texas A&M Energy Institute, Texas A&M UniversityCollege Station TX77843
| | - Baoguo Zhao
- PetroChina Dushanzi Petrochemical CompanyXinjiang833600 P. R. China
| | - Guangming Du
- PetroChina Dushanzi Petrochemical CompanyXinjiang833600 P. R. China
| | - Xin Su
- PetroChina Dushanzi Petrochemical CompanyXinjiang833600 P. R. China
| | - Hongwei Liu
- PetroChina Dushanzi Petrochemical CompanyXinjiang833600 P. R. China
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Kieslich CA, Smadbeck J, Khoury GA, Floudas CA. conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure. J Chem Inf Model 2016; 56:455-61. [DOI: 10.1021/acs.jcim.5b00566] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - James Smadbeck
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - George A. Khoury
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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Affiliation(s)
- Onur Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexander M. Niziolek
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station, Texas 77843, United States
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station, Texas 77843, United States
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22
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Li J, Xiao X, Floudas CA. Integrated gasoline blending and order delivery operations: Part I. short-term scheduling and global optimization for single and multi-period operations. AIChE J 2016. [DOI: 10.1002/aic.15168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jie Li
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77843
- Texas A&M Energy Institute; Texas A&M University; College Station TX 77843
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Xin Xiao
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Christodoulos A. Floudas
- Artie McFerrin Dept. of Chemical Engineering; Texas A&M University; College Station TX 77843
- Texas A&M Energy Institute; Texas A&M University; College Station TX 77843
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Kieslich CA, Tamamis P, Guzman YA, Onel M, Floudas CA. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism. PLoS One 2016; 11:e0148974. [PMID: 26859389 PMCID: PMC4747591 DOI: 10.1371/journal.pone.0148974] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/26/2016] [Indexed: 01/21/2023] Open
Abstract
HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/.
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Affiliation(s)
- Chris A Kieslich
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Yannis A Guzman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States of America
| | - Melis Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
| | - Christodoulos A Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States of America.,Texas A&M Energy Institute, Texas A&M University, College Station, TX, United States of America
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24
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Zhang H, Huang Q, Bei Z, Wei Y, Floudas CA. COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming. Proteins 2016; 84:332-48. [PMID: 26756402 DOI: 10.1002/prot.24979] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/19/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022]
Abstract
In this article, we present COMSAT, a hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT consists of two modules: COMSAT_SVM which is trained mainly on position-specific scoring matrix features, and COMSAT_MILP which is an ab initio method based on optimization models. Contacts predicted by the SVM model are ranked by SVM confidence scores, and a threshold is trained to improve the reliability of the predicted contacts. For TM proteins with no contacts above the threshold, COMSAT_MILP is used. The proposed hybrid contact prediction scheme was tested on two independent TM protein sets based on the contact definition of 14 Å between Cα-Cα atoms. First, using a rigorous leave-one-protein-out cross validation on the training set of 90 TM proteins, an accuracy of 66.8%, a coverage of 12.3%, a specificity of 99.3% and a Matthews' correlation coefficient (MCC) of 0.184 were obtained for residue pairs that are at least six amino acids apart. Second, when tested on a test set of 87 TM proteins, the proposed method showed a prediction accuracy of 64.5%, a coverage of 5.3%, a specificity of 99.4% and a MCC of 0.106. COMSAT shows satisfactory results when compared with 12 other state-of-the-art predictors, and is more robust in terms of prediction accuracy as the length and complexity of TM protein increase. COMSAT is freely accessible at http://hpcc.siat.ac.cn/COMSAT/.
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Affiliation(s)
- Huiling Zhang
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Qingsheng Huang
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhendong Bei
- Center for Cloud Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yanjie Wei
- Centre for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Christodoulos A Floudas
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, 77843.,Texas A&M Energy Institute, Texas A&M University, College Station, Texas, 77843
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25
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Affiliation(s)
- Christodoulos A. Floudas
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843 USA
- Texas A&M Energy Institute, 302D Williams Administration Building, 3372 Texas A&M UniversityCollege Station TX77843USA
| | - Alexander M. Niziolek
- Dept. of Chemical and Biological EngineeringPrinceton UniversityPrinceton NJ08544 USA
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843 USA
- Texas A&M Energy Institute, 302D Williams Administration Building, 3372 Texas A&M UniversityCollege Station TX77843USA
| | - Onur Onel
- Dept. of Chemical and Biological EngineeringPrinceton UniversityPrinceton NJ08544 USA
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843 USA
- Texas A&M Energy Institute, 302D Williams Administration Building, 3372 Texas A&M UniversityCollege Station TX77843USA
| | - Logan R. Matthews
- Dept. of Chemical and Biological EngineeringPrinceton UniversityPrinceton NJ08544 USA
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M UniversityCollege Station TX77843 USA
- Texas A&M Energy Institute, 302D Williams Administration Building, 3372 Texas A&M UniversityCollege Station TX77843USA
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26
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Niziolek AM, Onel O, Floudas CA. Production of benzene, toluene, and xylenes from natural gas via methanol: Process synthesis and global optimization. AIChE J 2016. [DOI: 10.1002/aic.15144] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alexander M. Niziolek
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M University, College Station TX77843
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station TX77843
- Dept. of Chemical and Biological EngineeringPrinceton UniversityPrinceton NJ08544
| | - Onur Onel
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M University, College Station TX77843
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station TX77843
- Dept. of Chemical and Biological EngineeringPrinceton UniversityPrinceton NJ08544
| | - Christodoulos A. Floudas
- Artie McFerrin Dept. of Chemical EngineeringTexas A&M University, College Station TX77843
- Texas A&M Energy Institute, 302D Williams Administration Building 3372, Texas A&M University, College Station TX77843
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27
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Niziolek AM, Onel O, Floudas CA. Production of Benzene, Toluene, and the Xylenes from Natural Gas via Methanol. Computer Aided Chemical Engineering 2016. [DOI: 10.1016/b978-0-444-63428-3.50396-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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28
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Guzman YA, Matthews LR, Floudas CA. New a priori and a posteriori probabilistic bounds for robust counterpart optimization: I. Unknown probability distributions. Comput Chem Eng 2016. [DOI: 10.1016/j.compchemeng.2015.09.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Matthews LR, Niziolek AM, Onel O, Pinnaduwage N, Floudas CA. Biomass to Liquid Transportation Fuels via Biological and Thermochemical Conversion: Process Synthesis and Global Optimization Strategies. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b03319] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Logan R. Matthews
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexander M. Niziolek
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Onur Onel
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Neesha Pinnaduwage
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Texas A&M Energy Institute, Texas A&M University, College Station, Texas 77843-3372, United States
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30
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31
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Onel O, Niziolek AM, Floudas CA. Integrated biomass and fossil fuel systems towards the production of fuels and chemicals: state of the art approaches and future challenges. Curr Opin Chem Eng 2015. [DOI: 10.1016/j.coche.2015.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Niziolek AM, Onel O, Hasan MF, Floudas CA. Municipal solid waste to liquid transportation fuels – Part II: Process synthesis and global optimization strategies. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2014.10.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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Niziolek AM, Onel O, Elia JA, Baliban RC, Floudas CA. Coproduction of liquid transportation fuels and C6_C8aromatics from biomass and natural gas. AIChE J 2015. [DOI: 10.1002/aic.14726] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander M. Niziolek
- Dept. of Chemical and Biological Engineering; Princeton University; Princeton NJ 08544
| | - Onur Onel
- Dept. of Chemical and Biological Engineering; Princeton University; Princeton NJ 08544
| | - Josephine A. Elia
- Dept. of Chemical and Biological Engineering; Princeton University; Princeton NJ 08544
| | - Richard C. Baliban
- Dept. of Chemical and Biological Engineering; Princeton University; Princeton NJ 08544
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34
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Gorham R, Forest DL, Khoury GA, Smadbeck J, Beecher CN, Healy ED, Tamamis P, Archontis G, Larive C, Floudas CA, Radeke MJ, Johnson LV, Morikis D. New compstatin peptides containing N-terminal extensions and non-natural amino acids exhibit potent complement inhibition and improved solubility characteristics. J Med Chem 2015; 58:814-26. [PMID: 25494040 PMCID: PMC4306506 DOI: 10.1021/jm501345y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Indexed: 01/21/2023]
Abstract
Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions; however, poor solubility promotes aggregation in aqueous environments. We have designed new compstatin peptides derived from the W4A9 sequence (Ac-ICVWQDWGAHRCT-NH2, cyclized between C2 and C12), based on structural, computational, and experimental studies. Furthermore, we developed and utilized a computational framework for the design of peptides containing non-natural amino acids. These new compstatin peptides contain polar N-terminal extensions and non-natural amino acid substitutions at positions 4 and 9. Peptides with α-modified non-natural alanine analogs at position 9, as well as peptides containing only N-terminal polar extensions, exhibited similar activity compared to W4A9, as quantified via ELISA, hemolytic, and cell-based assays, and showed improved solubility, as measured by UV absorbance and reverse-phase HPLC experiments. Because of their potency and solubility, these peptides are promising candidates for therapeutic development in numerous complement-mediated diseases.
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Affiliation(s)
- Ronald
D. Gorham
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
| | - David L. Forest
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - George A. Khoury
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Consuelo N. Beecher
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Evangeline D. Healy
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Phanourios Tamamis
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Georgios Archontis
- Department
of Physics, University of Cyprus, PO20537, CY1678 Nicosia, Cyprus
| | - Cynthia
K. Larive
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Christodoulos A. Floudas
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Monte J. Radeke
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Lincoln V. Johnson
- Center
for the Study of Macular Degeneration, Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
| | - Dimitrios Morikis
- Department
of Bioengineering, University of California, Riverside, California 92521, United States
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35
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Onel O, Niziolek AM, Elia JA, Baliban RC, Floudas CA. Biomass and Natural Gas to Liquid Transportation Fuels and Olefins (BGTL+C2_C4): Process Synthesis and Global Optimization. Ind Eng Chem Res 2015. [DOI: 10.1021/ie503979b] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Onur Onel
- Department of Chemical and
Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Alexander M. Niziolek
- Department of Chemical and
Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Josephine A. Elia
- Department of Chemical and
Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Richard C. Baliban
- Department of Chemical and
Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Department of Chemical and
Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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36
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37
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Floudas CA, Pistikopoulos EN. Professor Ignacio E. Grossmann—Tribute. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2014.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Khoury GA, Smadbeck J, Tamamis P, Vandris AC, Kieslich CA, Floudas CA. Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family. ACS Synth Biol 2014; 3:855-69. [PMID: 24932669 PMCID: PMC4277759 DOI: 10.1021/sb400168u] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA . The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions.
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Affiliation(s)
- George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Andrew C. Vandris
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Chris A. Kieslich
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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39
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Khoury GA, Bhatia N, Floudas CA. Hydration free energies calculated using the AMBER ff03 charge model for natural and unnatural amino acids and multiple water models. Comput Chem Eng 2014. [DOI: 10.1016/j.compchemeng.2014.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Onel O, Niziolek AM, Hasan MF, Floudas CA. Municipal solid waste to liquid transportation fuels – Part I: Mathematical modeling of a municipal solid waste gasifier. Comput Chem Eng 2014. [DOI: 10.1016/j.compchemeng.2014.03.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Croker DE, Halai R, Kaeslin G, Morikis D, Woodruff T, Floudas CA, Monk PN, Cooper MA. 32. Cytokine 2014. [DOI: 10.1016/j.cyto.2014.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Li Z, Floudas CA. Optimal scenario reduction framework based on distance of uncertainty distribution and output performance: I. Single reduction via mixed integer linear optimization. Comput Chem Eng 2014. [DOI: 10.1016/j.compchemeng.2014.03.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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43
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Halai R, Bellows-Peterson ML, Branchett W, Smadbeck J, Kieslich CA, Croker DE, Cooper MA, Morikis D, Woodruff TM, Floudas CA, Monk PN. Derivation of ligands for the complement C3a receptor from the C-terminus of C5a. Eur J Pharmacol 2014; 745:176-81. [PMID: 25446428 PMCID: PMC4263610 DOI: 10.1016/j.ejphar.2014.10.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/14/2014] [Accepted: 10/22/2014] [Indexed: 01/09/2023]
Abstract
The complement cascade is a highly sophisticated network of proteins that are well regulated and directed in response to invading pathogens or tissue injury. Complement C3a and C5a are key mediators produced by this cascade, and their dysregulation has been linked to a plethora of inflammatory and autoimmune diseases. Consequently, this has stimulated interest in the development of ligands for the receptors for these complement peptides, C3a receptor, and C5a1 (C5aR/CD88). In this study we used computational methods to design novel C5a1 receptor ligands. However, functional screening in human monocyte-derived macrophages using the xCELLigence label-free platform demonstrated altered specificity of our ligands. No agonist/antagonist activity was observed at C5a1, but we instead saw that the ligands were able to partially agonize the closely related complement receptor C3a receptor. This was verified in the presence of C3a receptor antagonist SB 290157 and in a stable cell line expressing either C5a1 or C3a receptor alone. C3a agonism has been suggested to be a potential treatment of acute neutrophil-driven traumatic pathologies, and may have great potential as a therapeutic avenue in this arena.
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Affiliation(s)
- Reena Halai
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Will Branchett
- Department of Infection and Immunity, Sheffield University Medical School, Sheffield, UK
| | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Chris A Kieslich
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA; Department of Bioengineering, University of California, Riverside, CA, USA
| | - Daniel E Croker
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dimitrios Morikis
- Department of Bioengineering, University of California, Riverside, CA, USA
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christodoulos A Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
| | - Peter N Monk
- Department of Infection and Immunity, Sheffield University Medical School, Sheffield, UK.
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44
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Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem ACB, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN, Players F. WeFold: a coopetition for protein structure prediction. Proteins 2014; 82:1850-68. [PMID: 24677212 PMCID: PMC4249725 DOI: 10.1002/prot.24538] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 01/25/2014] [Accepted: 02/08/2014] [Indexed: 12/19/2022]
Abstract
The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at "coopetition" in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org.
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Affiliation(s)
- George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, USA
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Poland
| | - Firas Khatib
- Department of Biochemistry, University of Washington, USA
| | - Hongyi Zhou
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, USA
| | - Gaurav Chopra
- Department of Structural Biology, School of Medicine, Stanford University, USA
- Diabetes Center, School of Medicine, University of California San Francisco (UCSF), USA
| | - Jaume Bacardit
- School of Computing Science, Newcastle University, United Kingdom
| | - Leandro O. Bortot
- Laboratory of Biological Physics, Faculty of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, Brazil
| | - Rodrigo A. Faccioli
- Institute of Mathematical and Computer Sciences, University of São Paulo, Brazil
| | - Xin Deng
- Department of Computer Science, University of Missouri, USA
| | - Yi He
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Pawel Krupa
- Faculty of Chemistry, University of Gdansk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Jilong Li
- Department of Computer Science, University of Missouri, USA
| | - Magdalena A. Mozolewska
- Faculty of Chemistry, University of Gdansk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | | | - James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, USA
| | - Tomasz Wirecki
- Faculty of Chemistry, University of Gdansk, Poland
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Seth Cooper
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, USA
| | - Jeff Flatten
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, USA
| | - Kefan Xu
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, USA
| | - David Baker
- Department of Biochemistry, University of Washington, USA
| | - Jianlin Cheng
- Department of Computer Science, University of Missouri, USA
| | | | | | - Chen Keasar
- Departments of Computer Science and Life Sciences, Ben Gurion University of the Negev, Israel
| | - Michael Levitt
- Department of Structural Biology, School of Medicine, Stanford University, USA
| | - Zoran Popović
- Center for Game Science, Department of Computer Science & Engineering, University of Washington, USA
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, USA
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45
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Li Z, Floudas CA. A Comparative Theoretical and Computational Study on Robust Counterpart Optimization: III. Improving the Quality of Robust Solutions. Ind Eng Chem Res 2014; 53:13112-13124. [PMID: 25678740 PMCID: PMC4311936 DOI: 10.1021/ie501898n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/18/2014] [Accepted: 07/23/2014] [Indexed: 11/30/2022]
Abstract
In
this paper, we study the solution quality of robust optimization problems
when they are used to approximate probabilistic constraints and propose
a novel method to improve the quality. Two solution frameworks are
first compared: (1) the traditional robust optimization framework
which only uses the a priori probability bounds and (3) the approximation
framework which uses the a posteriori probability bound. We illustrate
that the traditional robust optimization method is computationally
efficient but its solution is in general conservative. On the other
hand, the a posteriori probability bound based method provides less
conservative solution but it is computationally more difficult because
a nonconvex optimization problem is solved. Based on the comparative
study of the two methods, we propose a novel iterative solution framework
which combines the advantage of the a priori bound and the a posteriori
probability bound. The proposed method can improve the solution quality
of traditional robust optimization framework without significantly
increasing the computational effort. The effectiveness of the proposed
method is illustrated through numerical examples and applications
in planning and scheduling problems.
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Affiliation(s)
- Zukui Li
- Department of Chemical and Materials Engineering, University of Alberta , Edmonton, AB T6G2 V4, Canada
| | - Christodoulos A Floudas
- Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States
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46
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Smadbeck J, Chan KH, Khoury GA, Xue B, Robinson RC, Hauser CAE, Floudas CA. De novo design and experimental characterization of ultrashort self-associating peptides. PLoS Comput Biol 2014; 10:e1003718. [PMID: 25010703 PMCID: PMC4091692 DOI: 10.1371/journal.pcbi.1003718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/31/2014] [Indexed: 12/19/2022] Open
Abstract
Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K*association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K*association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.
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Affiliation(s)
- James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Kiat Hwa Chan
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Bo Xue
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | | | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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47
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Abstract
The economic, environmental, and social performances of energy systems depend on their geographical locations and the surrounding market infrastructure for feedstocks and energy products. Strategic decisions to locate energy conversion facilities must take all upstream and downstream operations into account, prompting the development of supply chain modeling and optimization methods. This article reviews the contributions of energy supply chain studies that include heat, power, and liquid fuels production. Studies are categorized based on specific features of the mathematical model, highlighting those that address energy supply chain models with and without considerations of multiperiod decisions. Studies that incorporate uncertainties are discussed, and opportunities for future research developments are outlined.
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Affiliation(s)
- Josephine A. Elia
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544
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48
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Niziolek AM, Onel O, Elia JA, Baliban RC, Xiao X, Floudas CA. Coal and Biomass to Liquid Transportation Fuels: Process Synthesis and Global Optimization Strategies. Ind Eng Chem Res 2014. [DOI: 10.1021/ie500505h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander M. Niziolek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Onur Onel
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Josephine A. Elia
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Richard C. Baliban
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Xin Xiao
- Langfang
Engineering and Technology Centre, National Engineering Laboratory for Hydrometallurgical Cleaner Production Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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49
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Abstract
The binding of protein HIV-1 gp120 to coreceptors CCR5 or CXCR4 is a key step of the HIV-1 entry to the host cell, and is predominantly mediated through the V3 loop fragment of HIV-1 gp120. In the present work, we delineate the molecular recognition of chemokine receptor CCR5 by a dual tropic HIV-1 gp120 V3 loop, using a comprehensive set of computational tools predominantly based on molecular dynamics simulations and free energy calculations. We report, what is to our knowledge, the first complete HIV-1 gp120 V3 loop : CCR5 complex structure, which includes the whole V3 loop and the N-terminus of CCR5, and exhibits exceptional agreement with previous experimental findings. The computationally derived structure sheds light into the functional role of HIV-1 gp120 V3 loop and CCR5 residues associated with the HIV-1 coreceptor activity, and provides insights into the HIV-1 coreceptor selectivity and the blocking mechanism of HIV-1 gp120 by maraviroc. By comparing the binding of the specific dual tropic HIV-1 gp120 V3 loop with CCR5 and CXCR4, we observe that the HIV-1 gp120 V3 loop residues 13-21, which include the tip, share nearly identical structural and energetic properties in complex with both coreceptors. This result paves the way for the design of dual CCR5/CXCR4 targeted peptides as novel potential anti-AIDS therapeutics.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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50
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Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA. De novo peptide design and experimental validation of histone methyltransferase inhibitors. PLoS One 2014; 9:e95535. [PMID: 24740276 PMCID: PMC3989331 DOI: 10.1371/journal.pone.0095535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histones are small proteins critical to the efficient packaging of DNA in the nucleus. DNA–protein complexes, known as nucleosomes, are formed when the DNA winds itself around the surface of the histones. The methylation of histone residues by enhancer of zeste homolog 2 (EZH2) maintains gene repression over successive cell generations. Overexpression of EZH2 can silence important tumor suppressor genes leading to increased invasiveness of many types of cancers. This makes the inhibition of EZH2 an important target in the development of cancer therapeutics. We employed a three-stage computational de novo peptide design method to design inhibitory peptides of EZH2. The method consists of a sequence selection stage and two validation stages for fold specificity and approximate binding affinity. The sequence selection stage consists of an integer linear optimization model that was solved to produce a rank-ordered list of amino acid sequences with increased stability in the bound peptide-EZH2 structure. These sequences were validated through the calculation of the fold specificity and approximate binding affinity of the designed peptides. Here we report the discovery of novel EZH2 inhibitory peptides using the de novo peptide design method. The computationally discovered peptides were experimentally validated in vitro using dose titrations and mechanism of action enzymatic assays. The peptide with the highest in vitro response, SQ037, was validated in nucleo using quantitative mass spectrometry-based proteomics. This peptide had an IC50 of 13.5 mM, demonstrated greater potency as an inhibitor when compared to the native and K27A mutant control peptides, and demonstrated competitive inhibition versus the peptide substrate. Additionally, this peptide demonstrated high specificity to the EZH2 target in comparison to other histone methyltransferases. The validated peptides are the first computationally designed peptides that directly inhibit EZH2. These inhibitors should prove useful for further chromatin biology investigations.
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