Design, docking, and evaluation of multiple libraries against multiple targets

Proteins: Structure, Function and Genetics

Volumn 42, Issue 3, 2001, Pages 296-318

  Lamb, Michelle L ^a   Burdick, Keith W ^a   Toba, Samuel ^a   Young, Malin M ^a   Geoffrey Skillman, A ^b   Zou, Xiaoqin ^a   Arnold, James R ^a   Kuntz, Irwin D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NONE   (United States)

Author keywords

Combinatorial library; Docking; Drug design; Scoring; Screening; Serine protease

Indexed keywords

BENZODIAZEPINE DERIVATIVE; CHYMOTRYPSIN; ELASTASE; PEPTIDE DERIVATIVE; PEPTIDE LIBRARY; TETRAHYDROISOQUINOLINE DERIVATIVE; TRYPSIN;

ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACIDS; ANIMALS; BINDING SITES; CATTLE; CHYMOTRYPSIN; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; ENZYME INHIBITORS; MODELS, MOLECULAR; MUTATION; PEPTIDE LIBRARY; PEPTIDES; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS; TRYPSIN;

EID: 0035865951     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010215)42:3<296::AID-PROT20>3.0.CO;2-F     Document Type: Article

References (73)

1. CombiDOCK: Structure-based combinatorial docking and library design
2. Inclusion of solvation in ligand binding free energy calculations using the generalized-born model
3. Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries
4. Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions
5. Combinatorial chemistry and molecular diversity. An overview
6. Structure-based drug design
7. Structure-based drug design: Computational advances
8. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D
9. Potent, low-molecular-weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II
10. Pro-Select: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
11. Combinatorial synthesis of small organic molecules
12. Virtual screening - An overview
13. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors
14. Identification of potent inhibitors of Plasmodium Falciparum plasmepsin II from an encoded statine combinatorial library
15. Rational design and combinatorial evaluation of enzyme inhibitor scaffolds: Identification of novel inhibitors of matrix metalloproteinases
16. Structure-activity relationship homology (SARAH): A conceptual framework for drug discovery in the genomic era
17. Predicting ligand binding to proteins by affinity fingerprinting
18. Protein affinity map of chemical space
19. Molecular similarity based on DOCK-generated fingerprints
20. The Protein Data Bank
21. 100,000 Protein structures for the biologist
22. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
23. Semianalytical treatment of solvation for molecular mechanics and dynamics
24. Discovery of protease inhibitors using targeted libraries
25. Comprehensive survey of combinatorial library synthesis: 1999
26. Molecular recognition of protein-ligand complexes: Applications to drug design
27. On the size of the active site in proteases. I. Papain
28. 1 cavities of serine proteinases
29. 1 variants of eglin c and of Turkey ovomucoid third domain with serine proteinases
30. 1 residues of substrates and of inhibitors in complexes with serine proteinases
31. 1 variants of bovine pancreatic trypsin inhibitor to four serine proteases
32. Critical evaluation of search algorithms for automated molecular docking and database screening
33. Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid B-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): Engineering of inhibitors with altered specificities
34. Crystal structure of an elastase-specific inhibitor elafin complexed with porcine pancreatic elastase determined at 1.9 angstroms resolution
35. Atomic structure of the trypsin-A90720A complex: A unified approach to structure and function
36. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
37. Automated docking with grid-based energy evaluation
38. Areas, volumes, packing, and protein structure
39. Solvent-accessible surfaces of proteins and nucleic acids
40. Analytical molecular surface calculation
41. The MIDAS display system
42. Geometric approach to macromolecule-ligand interactions
43. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
44. Rapid generation of high quality approximate 3-dimension molecular structures
45. Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
46. Crystal and molecular structures of the complex of α-chymotrypsin with its inhibitor Turkey ovomucoid third domain at 1.8 A resolution
47. Crystal structure of the bovine α-chymotrypsin: Kunitz inhibitor complex. An example of multiple protein: Protein recognition sites
48. The molecular structure of the complex of ascaris chymotrypsin/elastase inhibitor with porcine elastase
49. The geometry of the reactive site and of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
50. The maximal affinity of ligands
51. Preparation of chemically mutated aprotinin homologues by semi-synthesis: P1 substitutions change inhibitory specificity
52. Proton NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
53. pH-dependent processes in proteins
54. Accommodating protein flexibility in computational drug design
55. Analogous inhibitors of elastase do not always bind analogously
56. Interaction of aromatic compounds with alpha-chymotrypsin
57. Design, synthesis and evaluation of small-molecule combinatorial libraries
58. Solid-phase synthesis, characterization, and screening of a 43,000-compound tetrahydroisoquinoline combinatorial library
59. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
60. Enhancing the drug discovery process by integration of high-throughput chemistry and structure-based drug design
61. Computational analysis of the binding of P1 variants of domain 3 of Turkey ovomucoid inhibitor to streptomyces griseus protease B
62. Contributions of each contact residue in a standard mechanism canonical inhibitor
63. CAVEAT: A program to facilitate the design of organic molecules
64. Development of filter functions for protein-ligand docking