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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Journal ArticleDOI
Inhibition of Protein Kinase CK2 by Flavonoids and Tyrphostins. A Structural Insight.
Graziano Lolli,Giorgio Cozza,Marco Mazzorana,Elena Tibaldi,Luca Cesaro,Arianna Donella-Deana,Flavio Meggio,Andrea Venerando,Cinzia Franchin,Stefania Sarno,Roberto Battistutta,Lorenzo A. Pinna +11 more
TL;DR: The crystal structure of apigenin and luteolin in complex with the catalytic subunit of Zea mays CK2 has been solved, revealing their ability to interact with both the hinge region (Val116) and the positive area near Lys68 and the conserved water W1, the two main polar ligand anchoring points in the CK2 active site.
Journal ArticleDOI
Scoring functions for protein-ligand interactions: a critical perspective.
Tanja Schulz-Gasch,Martin Stahl +1 more
TL;DR: An overview of the current state of the field is given and key issues for the further development of scoring functions are outlined, including correct prediction of binding modes and high numbers of false positives.
Journal ArticleDOI
Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking.
TL;DR: A binary decision tree is developed to decide which protein structure to dock the ligand into, such that each ligand needs to be docked only once, leading to successful SOM prediction in 80% of the substrates.
Journal ArticleDOI
General Multiobjective Force Field Optimization Framework, with Application to Reactive Force Fields for Silicon Carbide.
TL;DR: The flexible and open architecture of GARFfield enables efficient and fast parallel optimization of parameters from quantum mechanical data sets for demanding applications like ReaxFF, electronic fast forward, and others including atomistic reactive charge-optimized many-body interatomic potentials, Morse, and coarse-grain force fields.
Journal ArticleDOI
ConsDock: A new program for the consensus analysis of protein-ligand interactions.
Nicodéme Paul,Didier Rognan +1 more
TL;DR: A consensus docking approach that takes advantage of three widely used docking tools (Dock, FlexX, and Gold) and significantly outperforms single docking with respect to the docking accuracy of the top‐ranked pose.
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