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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Adenosine mimetics as inhibitors of NAD+-dependent histone deacetylases, from kinase to sirtuin inhibition
Johannes Trapp,Anne Jochum,Rene Meier,Laura Saunders,Brett Marshall,Conrad Kunick,Eric Verdin,Peter G. Goekjian,Wolfgang Sippl,Manfred Jung +9 more
TL;DR: This work presents a systematic approach using adenosine mimics from one cofactor class (kinase inhibitors) as a viable method to generate new lead structures in another co Factor class (sirtuin inhibitors) that has broad implications for medicinal chemistry and specifically for sirtuin inhibitor design.
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Structure-activity studies on splitomicin derivatives as sirtuin inhibitors and computational prediction of binding mode.
Robert C. Neugebauer,Urszula Uchiechowska,Rene Meier,Henning Hruby,Vassil Valkov,Eric Verdin,Wolfgang Sippl,Manfred Jung +7 more
TL;DR: Protein-based virtual screening resulted in the identification of a novel Sirt2 inhibitor chemotype and selected inhibitors showed antiproliferative properties and tubulin hyperacetylation in MCF7 breast cancer cells and are promising candidates for further optimization as potential anticancer drugs.
Journal ArticleDOI
DARWIN: a program for docking flexible molecules.
TL;DR: A new program named “DARWIN” has been developed to perform docking calculations with proteins and other biological molecules, which uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex.
Journal ArticleDOI
Limitations and lessons in the use of X-ray structural information in drug design.
TL;DR: Some of the uncertainties introduced during the process of deriving an atomic model from the experimentally observed electron density are highlighted with recent examples from the literature, together with snippets of advice for the medicinal chemist embarking on using X-ray crystal structure information in a drug discovery programme.
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Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.
Tim ten Brink,Thomas E. Exner +1 more
TL;DR: This work presents a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS, demonstrating that both docking programs have problems in identifying the correct protomers.
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