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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Importance of Ligand Reorganization Free Energy in Protein-Ligand Binding-Affinity Prediction
TL;DR: This study demonstrates that ligand reorganization free energy plays an important role in the overall binding free energy between Smac mimetics and XIAP, and should be evaluated for other ligand-protein systems.
Journal ArticleDOI
The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case.
TL;DR: A modeling protocol that includes incremental conformational flexibility of the ligand and predicted water interactions and repeating the docking simulations in each of the seemingly identical binding sites of the multivalent toxin increases the chance of finding the correct binding mode.
Journal ArticleDOI
Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies
TL;DR: In this paper, a docking-based comparative intermolecular contacts analysis (dbCICA) is proposed to evaluate the consistency of docking by assessing the correlation between ligands affinities and their contacts with binding site spots.
Journal ArticleDOI
Selective Inhibitors of the Protein Tyrosine Phosphatase Shp2 Block Cellular Motility and Growth of Cancer Cells in Vitro and in Vivo.
Stefanie Grosskopf,Stefanie Grosskopf,Stefanie Grosskopf,Chris Eckert,Chris Eckert,Christoph Arkona,Silke Radetzki,Kerstin Böhm,Udo Heinemann,Gerhard Wolber,Jens-Peter von Kries,Walter Birchmeier,Jörg Rademann,Jörg Rademann +13 more
TL;DR: In cell culture experiments compound 25 was found to block hepatocyte growth factor‐stimulated epithelial–mesenchymal transition of human pancreatic adenocarcinoma (HPAF) cells, and strengthens the hypothesis that SHP2 is a relevant protein target for the inhibition of mobility and invasiveness of cancer cells.
Journal ArticleDOI
Synthesis, biological evaluation and docking studies of 4-amino substituted 1H-pyrazolo[3,4-d]pyrimidines.
Silvia Schenone,Chiara Brullo,Olga Bruno,Francesco Bondavalli,Luisa Mosti,Giovanni Maga,Emmanuele Crespan,Fabio Carraro,Fabrizio Manetti,Cristina Tintori,Maurizio Botta +10 more
TL;DR: Some compounds emerged as good dual inhibitors of the two enzymes, showed antiproliferative effects on two Bcr-Abl positive leukemia cell lines K-562 and KU-812, and induced apoptosis, as demonstrated by the PARP assay.
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