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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Binding site characteristics in structure-based virtual screening: evaluation of current docking tools
Tanja Schulz-Gasch,Martin Stahl +1 more
TL;DR: Two new docking programs FRED and Glide in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets in order to assess their accuracy in virtual screening.
Journal ArticleDOI
Comparison of Automated Docking Programs as Virtual Screening Tools
TL;DR: For a given docking method, hit rates were improved versus what would be expected for random selection for most protein targets, but the ability to prioritize known ligands on the basis of docking poses that resemble known crystal structures is both method- and target-dependent.
Journal ArticleDOI
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field
Sérgio F. Sousa,António J. M. Ribeiro,João Coimbra,Rui P. P. Neves,Silvia A. Martins,N.S.H.N. Moorthy,Pedro A. Fernandes,Maria J. Ramos +7 more
TL;DR: Current challenges in the field of protein-ligand docking such as the treatment of protein flexibility, the presence of structural water molecules and its effect in docking, and the entropy of binding are dissected and discussed, trying to anticipate the next years in this field.
Journal ArticleDOI
MM-GB/SA rescoring of docking poses in structure-based lead optimization.
TL;DR: The aim of this work is to evaluate the performance of the MM-GB/SA rescoring of docking poses in structure-based lead optimization and qualifies this approach as a more attractive alternative for rank-ordering than the Free Energy Perturbation and Thermodynamic Integration methodologies because it can handle more structurally dissimilar ligands and provides results at a fraction of the computational cost.
Journal ArticleDOI
Identification of 1,5-naphthyridine derivatives as a novel series of potent and selective TGF-beta type I receptor inhibitors.
Francoise Jeanne Gellibert,James Michael Woolven,‡ Marie-Hélène Fouchet,Neil Mathews,Helen Susanne Goodland,Victoria Lucy Helen Lovegrove,Alain Laroze,‡ Van-Loc Nguyen,Stéphane Sautet,Ruolan Wang,C. A. Janson,Ward Smith,Gael Krysa,Valerie Boullay,Anne-Charlotte De Gouville,Stéphane Huet,David Hartley +16 more
TL;DR: Compounds 15 and 19, which inhibited ALK5 autophosphorylation with IC50 = 6 and 4 nM, respectively, showed potent activities in both binding and cellular assays and exhibited selectivity over p38 mitogen-activated protein kinase.
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