Docking unbound proteins using shape complementarity, desolvation, and electrostatics

Proteins: Structure, Function and Genetics

Volumn 47, Issue 3, 2002, Pages 281-294

  Chen, Rong ^a   Weng, Zhiping ^b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; ANTIGEN; LIGAND; RECEPTOR;

ALGORITHM; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; ELECTRICITY; FOURIER TRANSFORMATION; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SOLVATION;

ALGORITHMS; ANIMALS; BINDING SITES; ELECTROSTATICS; FOURIER ANALYSIS; HUMANS; MACROMOLECULAR SUBSTANCES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS;

RUMEX;

EID: 0037093643     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10092     Document Type: Article

References (45)

1. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
2. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinatiohs between the yeast proteins
3. Proteomics to study genes and genomes
4. Protein therapeutics: Promises and challenges for the 21st century
5. Structural genomics: Beyond the human genome project
6. The Protein Data Bank
7. Protein docking algorithms: Simulating molecular recognition
8. Protein-protein recognition
9. Predicting the structure of protein complexes: A step in the right direction
10. Predictive docking of protein-protein and protein-DNA complexes
11. Protein-protein docking. Generation and filtering of complexes
12. Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking
13. A geometry-based suite of molecular docking processes
14. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
15. Estimation and filtering of potential protein-protein docking positions
16. An analysis of conformational changes on protein-protein association: Implications for predictive docking
17. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy
18. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase [see comments]
19. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
20. A systematic study of low-resolution recognition in protein-protein complexes
21. Modelling protein docking using shape complementarity, electrostatics and biochemical information
22. Protein docking using continuum electrostatics and geometric fit
23. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
24. Evaluation of the CASP2 docking section
25. Soft docking: Matching of molecular surface cubes
26. Examination of shape complementarity in docking of unbound proteins
27. BIGGER: A new (soft) docking algorithm for predicting protein interactions
28. Protein docking using spherical polar Fourier correlations
29. Protein docking using a genetic algorithm
30. A continuum model for protein-protein interactions: Application to the docking problem
31. Prediction of protein complexes using empirical free energy functions
32. Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
33. Scoring docked conformations generated by rigid-body protein-protein docking
34. Protein docking along smooth association pathways
35. The interpretation of protein structures: Estimation of static accessibility
36. Optimal sampling of the rotation function
37. Determination of atomic desolvation energies from the structures of crystallized proteins
38. Consistency in structural energetics of protein folding and peptide recognition
39. Computational determination of side chain specificity for pockets in class I MHC molecules
40. Protein-protein recognition: Exploring the energy funnels near the binding sites
41. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
42. Shape complementarity at protein/protein interfaces
43. Analysis of protein-protein interaction sites using surface patches
44. The atomic structure of protein-protein recognition sites
45. Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem