Development of filter functions for protein-ligand docking

Journal of Molecular Graphics and Modelling

Volumn 16, Issue 3, 1998, Pages 121-132

  Stahl, Martin ^a   Böhm, Hans Joachim ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

Drug design; Molecular docking; Scoring functions; Structure prediction

Indexed keywords

DOCKING; FILTRATION; MOLECULAR STRUCTURE; PROTEINS;

SOLVENT-ACCESSIBLE SURFACE (SAS);

MOLECULAR GRAPHICS;

FUCOSE; GLUTATHIONE DERIVATIVE; GUANOSINE PHOSPHATE; HISTIDINE; LIGAND; METHOTREXATE; N ACETYLNEURAMINIC ACID; TYROSINE;

ARTICLE; CHEMICAL STRUCTURE; CONFORMATION; LIGAND BINDING; LIPOPHILICITY; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROCESSING; PROTEIN STRUCTURE;

CRYSTALLOGRAPHY, X-RAY; HUMANS; LIGANDS; PROTEIN CONFORMATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; SOFTWARE;

EID: 0032226476     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(98)00018-7     Document Type: Article

References (25)

1. Docking small-molecule ligands into active sites
2. Computational methods for biomolecular docking
3. Molecular docking towards drug discovery
4. A fast flexible docking method using an incremental construction algorithrn
5. Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention
6. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
7. Development and validation of a genetic algorithm for flexible docking
8. Critical evaluation of search algorithms for automated molecular docking and database screening
9. Evaluation of the CASP2 docking section
10. A geometric approach to macromolecule-ligand interactions
11. Docking of flexible ligands: Applications of AutoDock
12. Flexible protein-ligand docking by global energy optimization in internal cool dinates
13. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor corn plexes
14. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
15. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
16. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de-novo design or 3D-database search programs
17. Computational methods to predict binding free energy in ligand-receptor complexes
18. Current issues in de novo molecular design
19. CASP2 experiences with docking flexible ligands using FlexX
20. Cavity search: An algorithm for the isolation and display of cavity-like binding regions
21. The protein data bank: A computer-based archival file for macromolecular structures
22. MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
23. Bow many conformers are there for small n-alkanes? Consequenees of asymmetric deformation in GG' segment
24. Hammerhead: Fast, fully atttomated docking of flexible ligands to protein binding sites