DARWIN: A program for docking flexible molecules

Proteins: Structure, Function and Genetics

Volumn 41, Issue 2, 2000, Pages 173-191

  Taylor, Jeffrey S ^a   Burnett, Roger M ^a,b  

^a WISTAR INSTITUTE   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Antibody antigen recognition; Carbohydrate binding; Drug design; Genetic algorithm; Protein ligand interaction

Indexed keywords

CONCANAVALIN A; DOCKING PROTEIN; IMMUNOGLOBULIN F(AB) FRAGMENT; MONOCLONAL ANTIBODY;

ACCURACY; ALGORITHM; ARTICLE; CALCULATION; COMPLEX FORMATION; COMPUTER PROGRAM; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION;

ALGORITHMS; ANTIBODIES, MONOCLONAL; CONCANAVALIN A; CRYSTALLOGRAPHY, X-RAY; IMMUNOGLOBULIN FAB FRAGMENTS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 0034332970     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20001101)41:2<173::AID-PROT30>3.0.CO;2-3     Document Type: Article

References (46)

1. A geometric approach to macromolecule-ligand interactions
2. Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
3. CHARMM: A program for macromolecular energy, minimization and dynamics calculations
4. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions
5. Ligand docking to proteins with discrete side-chain flexibility
6. Monte Carlo docking with ubiquitin
7. Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study
8. Flexible docking and design
9. The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution
10. Image reconstruction reveals the complex molecular organization of adenovirus
11. Genetic algorithms: Principles of natural selection applied to computation
12. A revised potential-energy surface for molecular mechanics studies of carbohydrates
13. Conformational modeling of substrate binding to endocellulase E2 from Thermomonospora fusca
14. Molecular dynamics simulations of the N-linked oligosaccharide of the lectin from Erythrina corallodendron
15. The crystal structure of a Fab fragment to the melanoma-associated GD2 ganglioside
16. Melanoma antigens: Immunological and biological characterization and clinical significance
17. Genetic algorithms in parametric design of aircraft
18. Dynamic anticipatory routing in circuit-switched telecommunications networks
19. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
20. Development and validation of a genetic algorithm for flexible docking
21. Docking flexible molecules: A case study of three proteins
22. Flexible ligand docking using a genetic algorithm
23. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations
24. The development of versions 3 and 4 of the Cambridge Structure Database System
25. General atomic and molecular electronic structure system
26. New spherical-cutoff methods for long-range forces in macromolecular simulation
27. Atomic solvation parameters applied to molecular dynamics of proteins in solution
28. Empirical potentials and functions for protein folding and binding
29. Calculating the electrostatic potential of molecules in solution: Method and error assessment
30. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
31. Accurate calculation of hydration free energies using macroscopic solvent molecules
32. Protein docking and complementarity
33. Refined structure of Concanavalin A complexed with methyl α-D-mannopyranoside at 2.0 A resolution and comparison with the saccharide-free structure
34. Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution
35. Calorimetric study of concanavalin A binding to saccharides
36. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
37. Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment
38. Thermodynamics of oligosaccharide binding to a monoclonal antibody specific for a Salmonella O-antigen point to hydrophobic interactions in the binding site
39. Carbohydrate-binding proteins: Tertiary structures and protein-sugar interactions
40. Antibody-antigen complexes
41. Monoclonal IgA J539 binds galactopyranosyl antigens on its surface
42. Monoclonal antibody-defined correlations in melanoma between levels of G(D2) and G(D3) antigens and antibody-mediated cytotoxicity
43. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons