Efficient docking of peptides to proteins without prior knowledge of the binding site

Protein Science

Volumn 11, Issue 7, 2002, Pages 1729-1737

  Hetényi, Csaba ^a   Van Der Spoel, David ^b  

^a UNIVERSITY OF SZEGED   (Hungary)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Binding site; Complex; Drug research; Flexible ligand

Indexed keywords

BENZAMIDINE; CARBOXYPEPTIDASE A; CHYMOTRYPSIN; CYCLOPHILIN A; PEPTIDE; PROTEINASE; SUBTILISIN; TRYPSIN; TRYPSINOGEN; LIGAND; PROTEIN;

ALGORITHM; ARTICLE; COMPLEX FORMATION; COMPUTER PROGRAM; DRUG BINDING SITE; DRUG DESIGN; DRUG PROTEIN BINDING; ENERGY; GENOMICS; LIGAND BINDING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RELIABILITY; X RAY CRYSTALLOGRAPHY; BINDING SITE; BIOLOGY; METABOLISM; METHODOLOGY; PROTEIN BINDING;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; LIGANDS; PEPTIDES; PROTEIN BINDING; PROTEINS; SOFTWARE;

EID: 0036084259     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0202302     Document Type: Article

References (32)

1. Crystal structure of calcium-independent subtilisin BPN with restored thermal stability folded without the prodomain
2. Fast prediction and visualization of protein binding pockets
3. Fragment-based flexible ligand docking by evolutionary optimization
4. A second generation force field for the simulation of nucleic acids, proteins, and organic molecules
5. Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes
6. Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid
7. γ-chymotrypsin is a complex of γ-chymotrypsin with its own autolysis products
8. LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
9. Mapping of the possible binding sequences of two β-sheet breaker peptides on beta amyloid peptide of Alzheimer's disease
10. Structural analysis of zinc substitutions in the active site of thermolysin
11. VMD: Visual molecular dynamics
12. Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 Å resolution
13. Protein folding and peptide docking: A molecular modeling and global optimization approach
14. GROMACS 3.0: A package for molecular simulation and trajectory analysis
15. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
16. Electrostatic effects in proteins: Comparison of dielectric and charge models
17. 3 receptor extracellular domain: Search for ligand binding sites
18. Raster3D: Photorealistic molecular graphics
19. The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test-case
20. A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR-data
21. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
22. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
23. Bovine β-lactoglobulin modified by 3-hydroxyphtalic anhydride blocks the CD4 cell receptor for HIV
24. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
25. EUDOCK: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
26. Analysis and application of potential energy smoothing and search methods for global optimization
27. Crystallographic studies on apocarboxy-peptidase A and the complex with glycyl-L-tyrosine
28. Matching chemistry and shape in molecular docking
29. Ligand binding by antibody IgE Lb4: Assessment of binding site preferences using microcalorimetry, docking and free energy simulations
30. Active site binding modes of HIV-1 integrase inhibitors
31. Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics
32. Super-Star: Improved knowledge-based interaction fields for protein binding sites