Journal ArticleDOI
Development and validation of a genetic algorithm for flexible docking.
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TLDR
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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The Light and Dark Sides of Virtual Screening: What Is There to Know?
Aleix Gimeno,María José Ojeda-Montes,Sarah Tomás-Hernández,Adrià Cereto-Massagué,Raúl Beltrán-Debón,Miquel Mulero,Gerard Pujadas,Santiago Garcia-Vallvé +7 more
TL;DR: The most common methodologies used in virtual screening workflows are reviewed in order to both introduce the inexperienced researcher to new methodologies and advise the experienced researcher on how to prevent common mistakes and the improper usage of virtual screening methodologies.
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Selective structure-based virtual screening for full and partial agonists of the beta2 adrenergic receptor.
Chris de Graaf,Didier Rognan +1 more
TL;DR: Modifying the X-ray structure of the beta2 adrenergic receptor to reflect early conformational events in receptor activation led to a receptor model able to selectively retrieve full and partial agonists by structure-based virtual screening.
Journal ArticleDOI
Natural products as DNA methyltransferase inhibitors: a computer-aided discovery approach.
TL;DR: Experimental data is provided suggesting that two of the most prominent natural products associated with DNA methylation inhibition, (−)-epigallocathechin-3-gallate (EGCG) and curcumin, have little or no pharmacologically relevant inhibitory activity.
Journal ArticleDOI
Discovery of structurally diverse HIV-1 integrase inhibitors based on a chalcone pharmacophore.
Jinxia Deng,Tino W. Sanchez,Laith Q. Al-Mawsawi,Raveendra Dayam,Rosendo A. Yunes,Antonio Garofalo,Michael B. Bolger,Nouri Neamati +7 more
TL;DR: This study demonstrates the systematic use of pharmacophore technologies to discover novel structurally diverse inhibitors based on lead molecules that would exhibit poor characteristics in vivo and identifies compounds that have the potential to exhibit favorable pharmacokinetic and pharmacodynamic profiles.
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Discovery of two novel, small-molecule inhibitors of DNA methylation
Pawel Siedlecki,Regine Garcia Boy,Tanja Musch,Bodo Brueckner,Sandor Suhai,Frank Lyko,Piotr Zielenkiewicz +6 more
TL;DR: The two highest scoring structures were found to inhibit DNA methyltransferase activity in vitro and in vivo and validate the screening procedure and provide a useful basis for further rational drug development.
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