Residue frequencies and pairing preferences at protein-protein interfaces

Proteins: Structure, Function and Genetics

Volumn 43, Issue 2, 2001, Pages 89-102

  Glaser, Fabian ^a   Steinberg, David M ^a   Vakser, Ilya A ^b   Ben Tal, Nir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Knowledge based potentials; Molecular recognition; Protein docking; Protein modeling; Statistical energy functions

Indexed keywords

ALANINE; AMINO ACID; ASPARTIC ACID; GLUTAMINE; GLYCINE; LEUCINE; PROTEIN; SERINE; TRYPTOPHAN;

ARTICLE; COMPLEX FORMATION; ENERGY; HYDROPHOBICITY; MOLECULAR RECOGNITION; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACIDS; DATABASES, FACTUAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; STATISTICS;

EID: 0035342450     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H     Document Type: Article

References (45)

1. Hydrophobic bonding and accessible surface area in proteins
2. Principles of protein-protein recognition
3. The atomic structure of protein-protein recognition sites
4. Principles of protein-protein interactions
5. Distribution and complementarity of hydropathy in multisubunit proteins
6. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
7. Morphology of protein-protein interfaces
8. Hydrophobic docking: A proposed enhancement to molecular recognition techniques
9. A role for surface hydrophobicity in protein-protein recognition
10. Analysis of protein-protein interaction sites using surface patches
11. Prediction of protein-protein interaction sites using patch analysis
12. Cavities and packing at protein interfaces
13. Protein-protein interaction at crystal contacts
14. Shape complementarity at protein/protein interfaces
15. The basics of binding: Mechanisms of antigen recognition and mimicry by antibodies
16. Predictive docking of protein-protein and protein-DNA complexes
17. Classical electrostatics in biology and chemistry
18. Electrostatic complementarity at protein/protein interfaces
19. Electrostatic aspects of protein-protein interactions
20. Structure-derived potentials and protein simulations
21. Empirical potentials and functions for protein folding and binding
22. How do potentials derived from structural databases relate to "true" potentials?
23. Anatomy of hot spots in protein interfaces
24. Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers
25. Empirical solvent-mediated potentials hold for both intramolecular and inter-molecular inter-residue interactions
26. Hydrophobic patches on protein subunit interfaces: Characteristics and prediction
27. Use of pair potentials across protein interfaces in screening predicted docked complexes
28. A data set of protein-protein interfaces generated with a sequence-order-independent comparison technique
29. Protein domain interfaces: Characterization and comparison with oligomeric protein interfaces
30. Protein-protein crystal-packing contacts
31. Comparative protein modelling by satisfaction of spatial restraints
32. Richardson extrapolation and the bootstrap
33. A simple method for displaying the hydropathic character of a protein
34. Specific versus non-specific contacts in protein crystals
35. Solvation energy in protein folding and binding
36. Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences
37. Surface, subunit interfaces and interior of oligomeric proteins
38. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale
39. Contribution of hydrophobic interactions to protein stability
40. Folding proteins with a simple energy function and extensive conformational searching
41. Evaluation of the CASP2 docking section
42. Computer analysis of protein-protein interaction