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Tahıl G, Delorme F, Le Berre D, Monflier É, Sayede A, Tilloy S. Stereoisomers Are Not Machine Learning's Best Friends. J Chem Inf Model 2024; 64:5451-5469. [PMID: 38949069 DOI: 10.1021/acs.jcim.4c00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
This study addresses the challenge of accurately identifying stereoisomers in cheminformatics, which originates from our objective to apply machine learning to predict the association constant between cyclodextrin and a guest. Identifying stereoisomers is indeed crucial for machine learning applications. Current tools offer various molecular descriptors, including their textual representation as Isomeric SMILES that can distinguish stereoisomers. However, such representation is text-based and does not have a fixed size, so a conversion is needed to make it usable to machine learning approaches. Word embedding techniques can be used to solve this problem. Mol2vec, a word embedding approach for molecules, offers such a conversion. Unfortunately, it cannot distinguish between stereoisomers due to its inability to capture the spatial configuration of molecular structures. This study proposes several approaches that use word embedding techniques to handle molecular discrimination using stereochemical information on molecules or considering Isomeric SMILES notation as a text in Natural Language Processing. Our aim is to generate a distinct vector for each unique molecule, correctly identifying stereoisomer information in cheminformatics. The proposed approaches are then compared to our original machine learning task: predicting the association constant between cyclodextrin and a guest molecule.
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Affiliation(s)
- Gökhan Tahıl
- Centre de Recherche en Informatique de Lens (CRIL)Univ. Artois, CNRS, Centre de Recherche en Informatique de Lens (CRIL), F-62300 Lens, France
- Univ. Artois, CNRS, Centrale Lille, Univ. Lille, UMR 8181, Unité de Catalyse et Chimie du Solide (UCCS), rue Jean Souvraz, SP 18, F-62307 Lens Cedex, France
| | - Fabien Delorme
- Centre de Recherche en Informatique de Lens (CRIL)Univ. Artois, CNRS, Centre de Recherche en Informatique de Lens (CRIL), F-62300 Lens, France
| | - Daniel Le Berre
- Centre de Recherche en Informatique de Lens (CRIL)Univ. Artois, CNRS, Centre de Recherche en Informatique de Lens (CRIL), F-62300 Lens, France
| | - Éric Monflier
- Univ. Artois, CNRS, Centrale Lille, Univ. Lille, UMR 8181, Unité de Catalyse et Chimie du Solide (UCCS), rue Jean Souvraz, SP 18, F-62307 Lens Cedex, France
| | - Adlane Sayede
- Univ. Artois, CNRS, Centrale Lille, Univ. Lille, UMR 8181, Unité de Catalyse et Chimie du Solide (UCCS), rue Jean Souvraz, SP 18, F-62307 Lens Cedex, France
| | - Sébastien Tilloy
- Univ. Artois, CNRS, Centrale Lille, Univ. Lille, UMR 8181, Unité de Catalyse et Chimie du Solide (UCCS), rue Jean Souvraz, SP 18, F-62307 Lens Cedex, France
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2
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Barreto Gomes D, Galentino K, Sisquellas M, Monari L, Bouysset C, Cecchini M. ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies. J Chem Inf Model 2023; 63:407-411. [PMID: 36603846 PMCID: PMC9875305 DOI: 10.1021/acs.jcim.2c00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 01/07/2023]
Abstract
The accurate prediction of protein-ligand binding affinities is a fundamental problem for the rational design of new drug entities. Current computational approaches are either too expensive or inaccurate to be effectively used in virtual high-throughput screening campaigns. In addition, the most sophisticated methods, e.g., those based on configurational sampling by molecular dynamics, require significant pre- and postprocessing to provide a final ranking, which hinders straightforward applications by nonexpert users. We present a novel computational platform named ChemFlow to bridge the gap between 2D chemical libraries and estimated protein-ligand binding affinities. The software is designed to prepare a library of compounds provided in SMILES or SDF format, dock them into the protein binding site, and rescore the poses by simplified free energy calculations. Using a data set of 626 protein-ligand complexes and GPU computing, we demonstrate that ChemFlow provides relative binding free energies with an RMSE < 2 kcal/mol at a rate of 1000 ligands per day on a midsize computer cluster. The software is publicly available at https://github.com/IFMlab/ChemFlow.
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Affiliation(s)
- Diego
E. Barreto Gomes
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
- Department
of Physics, Auburn University, Auburn, Alabama 36849, United States
| | - Katia Galentino
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Marion Sisquellas
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Luca Monari
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Cédric Bouysset
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
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3
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Ruzmetov T, Montes R, Sun J, Chen SH, Tang Z, Chang CEA. Binding Kinetics Toolkit for Analyzing Transient Molecular Conformations and Computing Free Energy Landscapes. J Phys Chem A 2022; 126:8761-8770. [DOI: 10.1021/acs.jpca.2c05499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Talant Ruzmetov
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
| | - Ruben Montes
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
| | - Jianan Sun
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
| | - Si-Han Chen
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
| | - Zhiye Tang
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California at Riverside, Riverside, California92521, United States
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4
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Sun Z, Zheng L, Wang K, Huai Z, Liu Z. Primary vs secondary: Directionalized guest coordination in β-cyclodextrin derivatives. Carbohydr Polym 2022; 297:120050. [DOI: 10.1016/j.carbpol.2022.120050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 02/01/2023]
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5
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Suárez D, Díaz N. Amphiphilic cyclodextrins: Dimerization and diazepam binding explored by molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Chen YQ, Sheng YJ, Ding HM, Ma YQ. Efficient calculation of protein-ligand binding free energy with GFN methods: the power of cluster model. Phys Chem Chem Phys 2022; 24:14339-14347. [DOI: 10.1039/d2cp00161f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The protein-ligand interactions are crucial in many biochemical processes and biomedical applications, yet it still remains challenging to accurately calculating the binding free energy of their interactions. In this work,...
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Boonma T, Nutho B, Sungthong B, Sripadung P, Rungrotmongkol T, Nunthaboot N. Molecular insights into complex formation between scandenin and various types of β-cyclodextrin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Ali HS, Chakravorty A, Kalayan J, de Visser SP, Henchman RH. Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge. J Comput Aided Mol Des 2021; 35:911-921. [PMID: 34264476 PMCID: PMC8367938 DOI: 10.1007/s10822-021-00406-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Abstract
Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy-entropy (EE) method to calculate the host-guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host-guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) "Drugs of Abuse" Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol-1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Arghya Chakravorty
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jas Kalayan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Samuel P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
- Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.
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10
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Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory. Int J Mol Sci 2021; 22:ijms22105061. [PMID: 34064655 PMCID: PMC8151972 DOI: 10.3390/ijms22105061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé-Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.
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11
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Loo JSE, Yong AYY, Yong YN. The effect of multiple simulation parameters on MM/PBSA performance for binding affinity prediction of CB1 cannabinoid receptor agonists and antagonists. Chem Biol Drug Des 2020; 96:1244-1254. [PMID: 32462752 DOI: 10.1111/cbdd.13733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/22/2020] [Accepted: 05/16/2020] [Indexed: 12/29/2022]
Abstract
Both the inactive- and active-state CB1 receptor crystal structures have now been solved, allowing their application in various structure-based drug design methods. One potential method utilizing these crystal structures is the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method of predicting relative binding free.
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Affiliation(s)
- Jason S E Loo
- Center for Drug Discovery and Molecular Pharmacology, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia.,School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Amelia Y Y Yong
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Yen Nee Yong
- School of Pharmacy, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
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12
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Zhong S, Huang K, Luo S, Dong S, Duan L. Improving the performance of the MM/PBSA and MM/GBSA methods in recognizing the native structure of the Bcl-2 family using the interaction entropy method. Phys Chem Chem Phys 2020; 22:4240-4251. [DOI: 10.1039/c9cp06459a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Correct discrimination of native structure plays an important role in drug design. IE method significantly improves the performance of MM/PB(GB)SA method in discriminating native and decoy structures in protein–ligand/protein systems of Bcl-2 family.
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Affiliation(s)
- Susu Zhong
- School of Physics and Electronics
- Shandong Normal University
- Jinan
- China
| | - Kaifang Huang
- School of Physics and Electronics
- Shandong Normal University
- Jinan
- China
| | - Song Luo
- School of Physics and Electronics
- Shandong Normal University
- Jinan
- China
| | - Shuheng Dong
- School of Physics and Electronics
- Shandong Normal University
- Jinan
- China
| | - Lili Duan
- School of Physics and Electronics
- Shandong Normal University
- Jinan
- China
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13
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He P, Sarkar S, Gallicchio E, Kurtzman T, Wickstrom L. Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin. J Phys Chem B 2019; 123:8378-8386. [PMID: 31509409 DOI: 10.1021/acs.jpcb.9b07028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study investigates the role of hydration and its relationship to the conformational equilibrium of the host molecule β-cyclodextrin. Molecular dynamics simulations indicate that the unbound β-cyclodextrin exhibits two state behavior in explicit solvent due to the opening and closing of its cavity. In implicit solvent, these transitions are not observed, and there is one dominant conformation of β-cyclodextrin with an open cavity. Based on these observations, we investigate the hypothesis that the expulsion of thermodynamically unfavorable water molecules into the bulk plays an important role in controlling the accessibility of the closed macrostate at room temperature. We compare the results of the molecular mechanics analytical generalized Born plus nonpolar solvation approach to those obtained through grid inhomogeneous solvation theory analysis with explicit solvation to elucidate the thermodynamic forces at play. The work illustrates the use of continuum solvent models to tease out solvation effects related to the inhomogeneity and the molecular nature of water and demonstrates the key role of the thermodynamics of enclosed hydration in driving the conformational equilibrium of molecules in solution.
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Affiliation(s)
- Peng He
- Center for Biophysics & Computational Biology/ICMS, Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Sheila Sarkar
- Department of Science , Borough of Manhattan Community College, The City University of New York , New York , New York 10007 , United States
| | - Emilio Gallicchio
- Department of Chemistry , Brooklyn College, The City University of New York , Brooklyn , New York 11210 , United States.,Ph.D. Programs in Chemistry & Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Tom Kurtzman
- Department of Chemistry , Lehman College, The City University of New York , Bronx , New York 10468 , United States.,Ph.D. Programs in Chemistry & Biochemistry , The Graduate Center of the City University of New York , 365 Fifth Avenue , New York , New York 10016 , United States
| | - Lauren Wickstrom
- Department of Science , Borough of Manhattan Community College, The City University of New York , New York , New York 10007 , United States
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Enhanced Solubility and Anticancer Potential of Mansonone G By β-Cyclodextrin-Based Host-Guest Complexation: A Computational and Experimental Study. Biomolecules 2019; 9:biom9100545. [PMID: 31569832 PMCID: PMC6843486 DOI: 10.3390/biom9100545] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 11/17/2022] Open
Abstract
Mansonone G (MG), a plant-derived compound isolated from the heartwood of Mansonia gagei, possesses a potent antitumor effect on several kinds of malignancy. However, its poor solubility limits the use for practical applications. Beta-cyclodextrin (βCD), a cyclic oligosaccharide composed of seven (1→4)-linked α-D-glucopyranose units, is capable of encapsulating a variety of poorly soluble compounds into its hydrophobic interior. In this work, we aimed to enhance the water solubility and the anticancer activity of MG by complexation with βCD and its derivatives (2,6-di-O-methyl-βCD (DMβCD) and hydroxypropyl-βCD). The 90-ns molecular dynamics simulations and MM/GBSA-based binding free energy results suggested that DMβCD was the most preferential host molecule for MG inclusion complexation. The inclusion complex formation between MG and βCD(s) was confirmed by DSC and SEM techniques. Notably, the MG/βCDs inclusion complexes exerted significantly higher cytotoxic effect (~2–7 fold) on A549 lung cancer cells than the uncomplexed MG.
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15
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Zhong S, Huang K, Xiao Z, Sheng X, Li Y, Duan L. Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method. J Phys Chem B 2019; 123:8704-8716. [DOI: 10.1021/acs.jpcb.9b08064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Zhengrong Xiao
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Xiehuang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
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16
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Abstract
Quantification of noncovalent interactions is the key for the understanding of binding mechanisms, of biological systems, for the design of drugs, their delivery and for the design of receptors for separations, sensors, actuators, or smart materials.
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