Journal ArticleDOI
Development and validation of a genetic algorithm for flexible docking.
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GOLD (Genetic Optimisation for Ligand Docking) is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding.About:
This article is published in Journal of Molecular Biology.The article was published on 1997-04-04. It has received 5882 citations till now. The article focuses on the topics: Searching the conformational space for docking & Protein–ligand docking.read more
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Human Pregnane X Receptor Antagonists and Agonists Define Molecular Requirements for Different Binding Sites
Sean Ekins,Cheng Chang,Sridhar Mani,Matthew D. Krasowski,Erica J. Reschly,Manisha Iyer,Vladyslav Kholodovych,Ni Ai,William J. Welsh,Michael Sinz,Peter W. Swaan,Rachana Patel,Kenneth Bachmann +12 more
TL;DR: Combining computational and experimental data for different classes of molecules provided strong evidence for agonists and antagonists binding distinct regions on PXR, and bear significant implications for future discovery of molecules that are more selective and potent antagonists.
Journal ArticleDOI
Prediction of potential toxicity and side effect protein targets of a small molecule by a ligand-protein inverse docking approach.
Yu Zong Chen,C.Y. Ung +1 more
TL;DR: A ligand-protein inverse docking approach is used for computer-automated search of a protein cavity database to identify protein targets and results show that 83% of the experimentally known toxicity and side effect targets for these drugs are predicted.
Journal ArticleDOI
Searching techniques for databases of two- and three-dimensional chemical structures.
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AGL-Score: Algebraic Graph Learning Score for Protein-Ligand Binding Scoring, Ranking, Docking, and Screening.
Duc Duy Nguyen,Guo-Wei Wei +1 more
TL;DR: This study indicates that machine learning methods are powerful tools for molecular docking and virtual screening and indicates that spectral geometry or spectral graph theory has the ability to infer geometric properties.
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Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.
TL;DR: It is demonstrated that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases.
References
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Book
Genetic algorithms in search, optimization, and machine learning
TL;DR: In this article, the authors present the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields, including computer programming and mathematics.
Genetic algorithms in search, optimization and machine learning
TL;DR: This book brings together the computer techniques, mathematical tools, and research results that will enable both students and practitioners to apply genetic algorithms to problems in many fields.
Book
Adaptation in natural and artificial systems
TL;DR: Names of founding work in the area of Adaptation and modiication, which aims to mimic biological optimization, and some (Non-GA) branches of AI.
Book
Molecular theory of gases and liquids
TL;DR: Molecular theory of gases and liquids as mentioned in this paper, molecular theory of gas and liquids, Molecular theory of liquid and gas, molecular theories of gases, and liquid theory of liquids, مرکز