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Literature DB >> 18680357

Exploiting ordered waters in molecular docking.

Abstract

A current weakness in docking is the treatment of water-mediated protein-ligand interactions. We explore switching ordered water molecules "on" and "off" during docking screens of a large library. The method assumes additivity and scales linearly with the number of waters sampled despite the exponential growth in configurations. It is tested for ligand enrichment against 24 targets, exploring up to 256 water configurations. Water inclusion increased enrichment substantially for 12 targets, while most others were largely unaffected.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Ligands
Water

Year: 2008 PMID： 18680357 PMCID： PMC2719016 DOI： 10.1021/jm8006239

Source DB: PubMed Journal: J Med Chem ISSN： 0022-2623 Impact factor: 7.446

17 in total

1. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.

Authors: Fredrik Osterberg; Garrett M Morris; Michel F Sanner; Arthur J Olson; David S Goodsell
Journal: Proteins Date: 2002-01-01

2. UCSF Chimera--a visualization system for exploratory research and analysis.

Authors: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376

3. Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

Authors: Chris de Graaf; Pavel Pospisil; Wouter Pos; Gerd Folkers; Nico P E Vermeulen
Journal: J Med Chem Date: 2005-04-07 Impact factor: 7.446

4. Modeling water molecules in protein-ligand docking using GOLD.

Authors: Marcel L Verdonk; Gianni Chessari; Jason C Cole; Michael J Hartshorn; Christopher W Murray; J Willem M Nissink; Richard D Taylor; Robin Taylor
Journal: J Med Chem Date: 2005-10-06 Impact factor: 7.446

5. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.

Authors: Niu Huang; Chakrapani Kalyanaraman; John J Irwin; Matthew P Jacobson
Journal: J Chem Inf Model Date: 2006 Jan-Feb Impact factor: 4.956

6. Ligand-protein docking with water molecules.

Authors: Benjamin C Roberts; Ricardo L Mancera
Journal: J Chem Inf Model Date: 2008-01-23 Impact factor: 4.956

7. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

Authors: M L Raymer; P C Sanschagrin; W F Punch; S Venkataraman; E D Goodman; L A Kuhn
Journal: J Mol Biol Date: 1997-01-31 Impact factor: 5.469

8. Enzyme crystal structure in a neat organic solvent.

Authors: P A Fitzpatrick; A C Steinmetz; D Ringe; A M Klibanov
Journal: Proc Natl Acad Sci U S A Date: 1993-09-15 Impact factor: 11.205

9. The particle concept: placing discrete water molecules during protein-ligand docking predictions.

Authors: M Rarey; B Kramer; T Lengauer
Journal: Proteins Date: 1999-01-01

10. The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case.

Authors: W E Minke; D J Diller; W G Hol; C L Verlinde
Journal: J Med Chem Date: 1999-05-20 Impact factor: 7.446

28 in total

Exploiting ordered waters in molecular docking.

1. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock.

2. UCSF Chimera--a visualization system for exploratory research and analysis.

3. Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking.

4. Modeling water molecules in protein-ligand docking using GOLD.

5. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.

6. Ligand-protein docking with water molecules.

7. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm.

8. Enzyme crystal structure in a neat organic solvent.

9. The particle concept: placing discrete water molecules during protein-ligand docking predictions.

10. The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: heat-labile enterotoxin, a multivalent test case.

1. A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.

2. Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors.

Review 3. Docking Screens for Novel Ligands Conferring New Biology.

4. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions.

5. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.

6. Solvated protein-DNA docking using HADDOCK.

7. Insights from comprehensive multiple receptor docking to HDAC8.

8. DOCK 6: Impact of new features and current docking performance.

9. Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.

10. Automated docking screens: a feasibility study.