High throughput docking for library design and library prioritization

Proteins: Structure, Function and Genetics

Volumn 43, Issue 2, 2001, Pages 113-124

  Diller, David J ^a   Merz Jr , Kenneth M ^a  

^a PHARMACOPEIA INC   (United States)

Author keywords

Combinatorial chemistry; Conformational analysis; Flexible minimization; Molecular docking

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; PRIORITY JOURNAL; PRODUCTIVITY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; VALIDATION PROCESS;

BINDING SITES; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTATIONAL BIOLOGY; LIGANDS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0035342434     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010501)43:2<113::AID-PROT1023>3.0.CO;2-T     Document Type: Article

References (43)

1. Efficacy and selectivity in flexible database docking
2. Structure-based identification of small molecule antiviral compounds targeted to the gp41 core structure of the human immunodeficiency virus type 1
3. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
4. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
5. Automated docking of substrates to proteins by simulated annealing
6. Development and validation of a genetic algorithm for flexible docking
7. A comparison of heuristic search algorithms for molecular docking
8. Flexible docking using Tabu search and an empirical estimate of binding affinity
9. A critical evaluation of several global optimization algorithms for the purpose of molecular docking
10. A geometric approach to macromolecular-ligand interactions
11. Structure-based strategies for drug design and discovery
12. Automated flexible ligand docking method and its application for database search
13. A fast flexible docking method using an incremental construction algorithm
14. The particle concept: Placing discrete water molecules during protein-ligand docking predictions
15. Docking of hydrophobic ligands with interaction-based matching algorithms
16. Hammerhead: Fast fully automated docking of flexible ligands to protein binding sites
17. Receptor-based pharmacophore perception and modeling
18. Solvation energy in protein folding and binding
19. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
20. Effect of conformational flexibility and solvation on receptor-ligand binding free energies
21. Placement of medium-sized molecular fragments into active sites of proteins
22. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
23. The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
24. A variational-vector calculus approach to machine dynamics
25. Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
26. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
27. Crystal structures of HIV-2 protease in complex with inhibitors containing hydroxyethylamine dipeptide isostere
28. X-ray crystal structure of the HIV protease complex with L-700,417, an inhibitor with psuedo C2 symmetry
29. Molecular structure at 1.8 A of mouse liver class pi glutathione S-transferase complexed with S-(p-nitrobenzyl)glutathione and other inhibitors
30. Structures of aromatic inhibitors of influenza virus neuraminidase
31. The crystal strucutures ast 2.2-A resolution of hydroxyethyleene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
32. Identification of potent inhibitors of plasmodium falciparum plasmepsin II from an encoded statine combinatorial library
33. Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum
34. Analysis of conformational coverage. 2. Applications of conformational models
35. Analysis of conformational coverage. 1. Validation and estimation of coverage
36. A general and fast scoring function for protein-ligand interactions: A simplified potential approach
37. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
38. Semianalytical treatment of solvation for molecular mechanics and dynamics
39. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
40. An automated method for predicting the positions of hydrogen-bonding atoms in binding sites