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Guedes IA, Barreto AMS, Marinho D, Krempser E, Kuenemann MA, Sperandio O, Dardenne LE, Miteva MA. New machine learning and physics-based scoring functions for drug discovery. Sci Rep 2021; 11:3198. [PMID: 33542326 PMCID: PMC7862620 DOI: 10.1038/s41598-021-82410-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [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: 11/02/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different target classes. Scoring functions based on precise physics-based descriptors better representing protein–ligand recognition process are strongly needed. We developed a set of new empirical scoring functions, named DockTScore, by explicitly accounting for physics-based terms combined with machine learning. Target-specific scoring functions were developed for two important drug targets, proteases and protein–protein interactions, representing an original class of molecules for drug discovery. Multiple linear regression (MLR), support vector machine and random forest algorithms were employed to derive general and target-specific scoring functions involving optimized MMFF94S force-field terms, solvation and lipophilic interactions terms, and an improved term accounting for ligand torsional entropy contribution to ligand binding. DockTScore scoring functions demonstrated to be competitive with the current best-evaluated scoring functions in terms of binding energy prediction and ranking on four DUD-E datasets and will be useful for in silico drug design for diverse proteins as well as for specific targets such as proteases and protein–protein interactions. Currently, the MLR DockTScore is available at www.dockthor.lncc.br.
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Affiliation(s)
- Isabella A Guedes
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil.,Inserm U973, Université Paris Diderot, Paris, France
| | - André M S Barreto
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil
| | - Diogo Marinho
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil
| | | | | | - Olivier Sperandio
- Inserm U973, Université Paris Diderot, Paris, France.,Structural Bioinformatics Unit, CNRS UMR3528, Institut Pasteur, 75015, Paris, France
| | - Laurent E Dardenne
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil.
| | - Maria A Miteva
- Inserm U973, Université Paris Diderot, Paris, France. .,Inserm U1268 "Medicinal Chemistry and Translational Research", CiTCoM, UMR 8038, CNRS, Université de Paris, 75006, Paris, France.
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Albrecht SV, Barreto AMS, Braziunas D, Buckeridge DL, Cuayáhuitl H, Dethlefs N, Endres M, Farahmand AM, Fox M, Frommberger L, Ganzfried S, Gil Y, Guillet S, Hunter LE, Jhala A, Kersting K, Konidaris G, Lecue F, McIlraith S, Natarajan S, Noorian Z, Poole D, Ronfard R, Saffiotti A, Shaban-Nejad A, Srivastava B, Tesauro G, Uceda-Sosa R, Van den Broeck G, Van Otterlo M, Wallace BC, Weng P, Wiens J, Zhang J. Reports of the AAAI 2014 Conference Workshops. AI MAG 2015. [DOI: 10.1609/aimag.v36i1.2575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The AAAI-14 Workshop program was held Sunday and Monday, July 27–28, 2012, at the Québec City Convention Centre in Québec, Canada. Canada. The AAAI-14 workshop program included fifteen workshops covering a wide range of topics in artificial intelligence. The titles of the workshops were AI and Robotics; Artificial Intelligence Applied to Assistive Technologies and Smart Environments; Cognitive Computing for Augmented Human Intelligence; Computer Poker and Imperfect Information; Discovery Informatics; Incentives and Trust in Electronic Communities; Intelligent Cinematography and Editing; Machine Learning for Interactive Systems: Bridging the Gap between Perception, Action and Communication; Modern Artificial Intelligence for Health Analytics; Multiagent Interaction without Prior Coordination; Multidisciplinary Workshop on Advances in Preference Handling; Semantic Cities — Beyond Open Data to Models, Standards and Reasoning; Sequential Decision Making with Big Data; Statistical Relational AI; and The World Wide Web and Public Health Intelligence. This article presents short summaries of those events.
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