Structure-based combinatorial library design: Methodologies and applications

Journal of Molecular Graphics and Modelling

Volumn 20, Issue 6, 2002, Pages 463-468

  Beavers, Mary Pat ^a   Chen, Xin ^a  

^a R W JOHNSON PHARMACEUTICAL RES I   (United States)

Author keywords

Medicinal chemistry; Small focused libraries; X ray crystallography

Indexed keywords

NUCLEAR MAGNETIC RESONANCE; X RAY ANALYSIS;

COMBINATORIAL LIBRARY DESIGNS;

LOGIC DESIGN;

ASPARTIC PROTEINASE INHIBITOR; BENZAMIDINE DERIVATIVE; BENZODIAZEPINE; BLOOD CLOTTING FACTOR 10A; CATHEPSIN D; CHYMOTRYPSIN; ELASTASE; GLYCINE DERIVATIVE; PLASMEPSIN II; TETRAHYDROISOQUINOLINE; TRYPSIN; PEPTIDE LIBRARY; PROTEINASE INHIBITOR;

BINDING AFFINITY; BINDING SITE; COMBINATORIAL CHEMISTRY; COMBINATORIAL LIBRARY; COMPUTER PROGRAM; CONFERENCE PAPER; DATA BASE; DRUG CONFORMATION; DRUG DESIGN; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG SCREENING; DRUG TARGETING; EXPERIMENTAL DESIGN; LIGAND BINDING; MALARIA; METASTASIS; METHODOLOGY; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; PROTEIN TARGETING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SCORING SYSTEM; SEQUENCE HOMOLOGY; THREE DIMENSIONAL IMAGING; X RAY CRYSTALLOGRAPHY; ARTICLE; CHEMISTRY; STRUCTURE ACTIVITY RELATION;

BINDING SITES; CHEMISTRY, PHARMACEUTICAL; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; PEPTIDE LIBRARY; PROTEASE INHIBITORS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0036010704     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(01)00147-4     Document Type: Conference Paper

References (45)

1. Strategy and tactics in combinatorial organic synthesis. Application to drug discovery
2. Combinatorial synthesis of small organic molecules
3. High-throughput screening: Advances in assay technologies
4. Current and future trends in high throughput screening for drug discovery
5. Discovery of nanomolar ligands for 7-transmembrane G-protein-coupled receptors from a diverse N-(substituted) glycine peptoid library
6. Exploiting chemical libraries, structure and genomics in the search for kinase inhibitors
7. The design of small- and medium-sized focused combinatorial libraries
8. Structure-based strategies for drug design and discovery
9. Molecular recognition of protein-ligand complexes: Applications to drug design
10. Structure-based drug design
11. Inclusion of solvation in ligand binding free energy calculations using the generalized Born model
12. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
13. Database searching: Past, present and future
14. Docking: Predicting the structure and binding affinity of ligand-receptor complexes
15. Current computational tools for de novo ligand design
16. Current issues in de novo molecular design
17. Geometric approach to macromolecule-ligand interactions
18. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
19. A fast flexible docking method using an incremental construction algorithm
20. High throughput docking for library design and library prioritization
21. PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. Part 1. Technology
22. Molecular diversity in site-focused libraries
23. CombiDOCK: Structure-based combinatorial docking and library design
24. DREAM++: Flexible docking program for virtual combinatorial libraries
25. A recursive algorithm for efficient combinatorial library docking
26. Synergy between combinatorial chemistry and de novo design
27. Detailed analysis of scoring functions for virtual screening
28. Efficient electrostatic solvation model for protein-fragment docking
29. Semianalytical treatment of solvation for molecular mechanics and dynamics
30. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D
31. Potent, low-molecular weight non-peptide inhibitors of malarial aspartyl protease plasmepsin II
32. A second generation force field for the simulation of proteins, nucleic acids and organic molecules
33. Design, docking, and evaluation of multiple libraries against multiple targets
34. Binding of amino acid side chains to S1 cavities of serine proteinases
35. Interscaffolding additivity: Binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases
36. Combinatorial docking and combinatorial chemistry: Design of potent non-peptide thrombin inhibitors
37. The computer program LUDI: A new method for the de novo design of enzyme inhibitors
38. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
39. The design of phenylglycine containing benzamidine carboxamides as potent and selective inhibitors of factor Xa