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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Antiviral potential and molecular insight into neuraminidase inhibiting diarylheptanoids from Alpinia katsumadai.
Ulrike Grienke,Michaela Schmidtke,Johannes Kirchmair,Kathrin Pfarr,Peter Wutzler,Ralf Dürrwald,Gerhard Wolber,Klaus R. Liedl,Hermann Stuppner,Judith M. Rollinger +9 more
TL;DR: Docking results showed well-established interactions between the protein and the core of this novel NA-inhibiting natural scaffold, excellent surface complementarity to the simulated binding pocket, and concordance with experimentally derived SAR data.
Journal ArticleDOI
Potent Antimalarial Activity of Histone Deacetylase Inhibitor Analogues
Katherine T. Andrews,Thanh Nguyen Tran,Andrew J. Lucke,Pia Kahnberg,Giang Thanh Le,Glen M. Boyle,Donald L. Gardiner,Tina S. Skinner-Adams,Tina S. Skinner-Adams,David P. Fairlie +9 more
TL;DR: Results support PfHDAC enzymes as being promising targets for new antimalarial drug targets, based on homology modeling with human class I and class II HDAC enzymes.
Journal ArticleDOI
AADS--an automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors
TL;DR: A robust automated active site detection, docking, and scoring (AADS) protocol for proteins with known structures that predicts structure and energetics of the complexes agree quite well with experiment when tested on a data set of 170 protein-ligand complexes withknown structures and binding affinities.
Journal ArticleDOI
Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
Sean Ekins,Sean Ekins,Sandhya Kortagere,Manisha Iyer,Erica J. Reschly,Markus A. Lill,Matthew R. Redinbo,Matthew D. Krasowski +7 more
TL;DR: A comprehensive analysis focused on prediction of 115 steroids for ligand binding activity towards human PXR, illustrating modest success using the largest quantitative data set to date and multiple modeling approaches.
Journal ArticleDOI
Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy.
TL;DR: It is shown that using the protein structure from the complex that contains the bound ligand most similar to the docked ligand increases docking accuracy for all methods ("similarity selection"), and that models for predicting docking accuracy built using these parameters can be used to select the most appropriate docking method.
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