Protein-protein docking predictions for the CAPRI experiment

Proteins: Structure, Function and Genetics

Volumn 52, Issue 1, 2003, Pages 118-122

  Gray, Jeffrey J ^a,b   Moughon, Stewart E ^a   Kortemme, Tanja ^a   Schueler Furman, Ora ^a   Misura, Kira ^a   Morozov, Alexandre V ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b Johns Hopkins University   (United States)

Author keywords

Biomolecular free energy function; Flexible side chains; High resolution refinement; Protein binding; Protein interactions

Indexed keywords

DOCKING PROTEIN;

ARTICLE; COMPUTER PREDICTION; CONFORMATIONAL TRANSITION; ELECTRICITY; ENERGY; EXPERIMENT; HYDROGEN BOND; MODEL; MONTE CARLO METHOD; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE HOMOLOGY; SOLVATION; STATISTICS; TECHNIQUE;

ALGORITHMS; ALPHA-AMYLASE; AMINO ACID SEQUENCE; ANTIBODIES; ANTIGENS, VIRAL; BACTERIAL PROTEINS; BINDING SITES; CAPSID PROTEINS; EXOTOXINS; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; MACROMOLECULAR SUBSTANCES; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PROTEIN INTERACTION MAPPING; PROTEIN-SERINE-THREONINE KINASES; PROTEINS; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA; SEQUENCE ALIGNMENT;

EID: 0038697805     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10384     Document Type: Article

References (20)

1. Vajda S, Vakser IA, Sternberg MJ, Janin J. Modeling of protein interactions in genomes. Proteins 2002;47:444-446.
2. Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
3. Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 2000;97:10383-10388.
4. Dunbrack RL Jr, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
5. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
6. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
7. Koehl P, Delarue M. Polar and nonpolar atomic environments in the protein core: implications for folding and binding. Proteins 1994;20:264-278.
8. Ihaka R, Gentleman RR. A language for data analysis and graphics. J Comp Graph Stat 1996;5:299-314.
9. Misura K, Wedemeyer B, Baker D. Unpublished results (work in progress). 2002.
10. Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002;99:14116-14121.
11. Fieulaine S, Morera S, Poncet S, Monedero V, Gueguen-Chaignon V, Galinier A, Janin J, Deutscher J, Nessler S. X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotidebinding domain. EMBO J 2001;20:3917-3927.
12. Walker JE, Saraste M, Runswick MJ, Gay NJ. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1982;1:945-951.
13. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996;257:342-358.
14. Shi J, Innis CA, Chen L, Blundell TL. Evolutionary Trace Server (TraceSuite II). www-cryst.bioc.cam.ac.uk/~jiye/evoltrace/evoltrace. html, accessed September 2001.
15. Mathieu M, Petitpas I, Navaza J, Lepault J, Kohli E, Pothier P, Prasad BVV, Cohen J, Rey FA. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J 2001;20:1485-1497.
16. Wiley DC, Skehel JJ. The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu Rev Biochem 1987;56:365-394.
17. Li H, Llera A, Malchiodi EL, Mariuzza RA. The structural basis of T cell activation by superantigens. Annu Rev Immunol 1999;17:435-466.
18. Ortiz AR, Strauss CEM, Olmea O. MAMMOTH (Matching molecular models obtained from theory): an automated method for model comparison. Protein Sci 2002;11:2606-2621.
19. Li H, Llera A, Tsuchiya D, Leder L, Ysern X, Schlievert PM, Karjalainen K, Mariuzza RA. Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B. Immunity 1998;9:807-816.
20. Larsen TA, Olson AJ, Goodsell DS. Morphology of protein-protein interfaces. Structure 1998;6:421-427.