Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
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N. Budin
Abstract
A new computational approach for the efficient docking of flexible ligands in a rigid protein is presented. It exploits the binding modes of functional groups determined by an exhaustive search with solvation. The search in ligand conformational space is performed by a genetic algorithm whose scoring function approximates steric effects and intermolecular hydrogen bonds. Ligand conformations generated by the genetic algorithm are docked in the protein binding site by optimizing the fit of their fragments to optimal positions of chemically related functional groups. We show that the use of optimal binding modes of molecular fragments allows to dock known inhibitors with about ten rotatable bonds in the active site of the uncomplexed and complexed conformations of thrombin and HIV-1 protease.
Copyright © 2001 by Walter de Gruyter GmbH & Co. KG
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Articles in the same Issue
- Highlight: Evolution in Vivo, in Vitro and in Machina
- Modeling Genetic Networks and Their Evolution: A Complex Dynamical Systems Perspective
- Evolution in Silico and in Vitro: The RNA Model
- Divergent Evolution of (??)8-Barrel Enzymes
- RNA-Catalyzed Carbon-Carbon Bond Formation
- Toward Automated Nucleic Acid Enzyme Selection
- Duocalins: Engineered Ligand-Binding Proteins with Dual Specificity Derived from the Lipocalin Fold
- The Stochastic Evolution of Catalysts in Spatially Resolved Molecular Systems
- Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
- Specific Nucleoprotein Complexes within Adenovirus Capsids
- ERH (Enhancer of Rudimentary Homologue), a Conserved Factor Identical between Frog and Human, Is a Transcriptional Repressor
- Signal Transduction by the Chemokine Receptor CXCR5: Structural Requirements for G Protein Activation Analyzed by Chimeric CXCR1/CXCR5 Molecules
- Arginine-Specific Cysteine Proteinase from Porphyromonas gingivalis as a Convenient Tool in Protein Chemistry
- Chemokine-Induced Secretion of Gelatinase B in Primary Human Monocytes
