DOI: 10.1016/j.jmb.2004.02.040. ProMate: A Structure Based Prediction Program to Identify the Location of Protein

ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites

10.1016/j.jmb.2004.02.040

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Neuvirth, H., Raz, R., & Schreiber, G. (2004). ProMate: A Structure Based Prediction Program to Identify the Location of ProteinâProtein Binding Sites. Journal of Molecular Biology, 338(1), 181â199.

Authors 3

Hani Neuvirth (first)
Ran Raz (additional)
Gideon Schreiber (additional)

References 33 Referenced 358

10.1126/science.287.5456.1279 / Science / Convergent solutions to binding at a protein–protein interface by DeLano (2000)
10.1038/nsb1001-848 / Nature Struct. Biol. / Crystal structure and kinetic analysis of betalactamase inhibitor protein-II in complex with TEM-1 beta-lactamase by Lim (2001)
10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H / Proteins: Struct. Funct. Genet. / Residue frequencies and pairing preferences at protein-protein interfaces by Glaser (2001)
10.1002/(SICI)1097-0134(199707)28:3<333::AID-PROT4>3.0.CO;2-D / Proteins: Struct. Funct. Genet. / Hydrophobic patches on protein subunit interfaces: characteristics and prediction by Lijnzaad (1997)
10.1006/jmbi.1997.1233 / J. Mol. Biol. / Prediction of protein–protein interaction sites using patch analysis by Jones (1997)
10.1016/0079-6107(94)00008-W / Prog. Biophys. Mol. Biol. / Protein–protein interactions: a review of protein dimer structures by Jones (1995)
10.1006/jmbi.1998.2439 / J. Mol. Biol. / The atomic structure of proteinprotein recognition sites by Lo Conte (1999)
10.1002/prot.10085 / Proteins: Struct. Funct. Genet. / Dissecting protein–protein recognition sites by Chakrabarti (2002)
10.1002/pro.5560030501 / Protein Sci. / A role for surface hydrophobicity in protein–protein recognition by Young (1994)
{'key': '10.1016/j.jmb.2004.02.040_BIB10', 'series-title': 'Protein–Protein Recognition: Frontiers in Molecular Biology', 'author': 'Kleanthous', 'year': '2000'} / Protein–Protein Recognition: Frontiers in Molecular Biology by Kleanthous (2000)
10.1006/jmbi.1997.1234 / J. Mol. Biol. / Analysis of protein–protein interaction sites using surface patches by Jones (1997)
10.1110/ps.21302 / Protein Sci. / Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations by Ma (2002)
10.1093/protein/3.2.77 / Protein Eng. / The structure of interfaces between subunits of dimeric and tetrameric proteins by Miller (1989)
10.1002/(SICI)1097-0134(20000601)39:4<331::AID-PROT60>3.0.CO;2-A / Proteins: Struct. Funct. Genet. / Conservation of polar residues as hot spots at protein interfaces by Hu (2000)
10.1046/j.1432-1033.2002.02767.x / Eur. J. Biochem. / Prediction of protein–protein interaction sites in heterocomplexes with neural networks by Fariselli (2002)
10.1006/jmbi.2001.4870 / J. Mol. Biol. / Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking by Aloy (2001)
10.1002/prot.1099 / Proteins: Struct. Funct. Genet. / Prediction of protein interaction sites from sequence profile and residue neighbor list by Zhou (2001)
10.1016/S0022-2836(02)01336-0 / J. Mol. Biol. / An accurate, sensitive, and scalable method to identify functional sites in protein structures by Yao (2003)
10.1073/pnas.93.1.13 / Proc. Natl Acad. Sci. USA / Principles of protein–protein interactions by Jones (1996)
10.1006/jmbi.2000.3656 / J. Mol. Biol. / Evaluation of direct and cooperative contributions towards the strength of buried hydrogen bonds and salt bridges by Albeck (2000)
10.1093/protein/2.2.101 / Protein Eng. / An investigation of protein subunit and domain interfaces by Argos (1988)
10.1002/pro.5560050204 / Protein Sci. / PROMOTIF—a program to identify and analyze structural motifs in proteins by Hutchinson (1996)
10.1016/S0079-6107(01)00012-8 / Prog. Biophys. Mol. Biol. / Predicting properties of intrinsically unstructured proteins by Bright (2001)
10.1002/(SICI)1097-0134(199610)26:2<192::AID-PROT9>3.0.CO;2-I / Proteins: Struct. Funct. Genet. / A method for detecting hydrophobic patches on protein surfaces by Lijnzaad (1996)
{'key': '10.1016/j.jmb.2004.02.040_BIB25', 'first-page': '309', 'article-title': 'Refined crystal structure of the complex of subtilisin BPN′ and Streptomyces subtilisin inhibitor at 1.8Å resolution', 'volume': '221', 'author': 'Takeuchi', 'year': '1991', 'journal-title': 'J. Mol. Biol.'} / J. Mol. Biol. / Refined crystal structure of the complex of subtilisin BPN′ and Streptomyces subtilisin inhibitor at 1.8Å resolution by Takeuchi (1991)
10.1074/jbc.M002623200 / J. Biol. Chem. / A novel double-headed proteinaceous inhibitor for metalloproteinase and serine proteinase by Hiraga (2000)
10.1002/prot.1139 / Proteins: Struct. Funct. Genet. / New insights into the mechanism of protein–protein association by Selzer (2001)
10.1093/protein/gzh021 / PEDS / A novel method for scoring of docked protein complexes using predicted protein-protein binding sites by Gottschalk (2004)
10.1093/nar/28.1.235 / Nucl. Acids Res. / The Protein Data Bank by Berman (2000)
10.1093/protein/11.9.739 / Protein Eng. / Protein structure alignment by incremental combinatorial extension (CE) of the optimal path by Shindyalov (1998)
10.1093/nar/25.17.3389 / Nucl. Acids Res. / Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by Altschul (1997)
Efron, B. (1982). The Jackknife, The Bootstrap and Other Resampling Plans, SIAM, Philadelphia, PA. (10.1137/1.9781611970319)
10.1016/0263-7855(86)80086-8 / J. Mol. Graph. / Measurement of protein surface shape by solid angles by Connolly (1986)

Dates

Type	When
Created	21 years, 5 months ago (March 6, 2004, 6:41 a.m.)
Deposited	2 years, 4 months ago (April 27, 2023, 10:29 p.m.)
Indexed	3 days, 10 hours ago (Aug. 27, 2025, 12:20 p.m.)
Issued	21 years, 4 months ago (April 1, 2004)
Published	21 years, 4 months ago (April 1, 2004)
Published Print	21 years, 4 months ago (April 1, 2004)

Funders 0

None

BibTeX

@article{Neuvirth_2004, title={ProMate: A Structure Based Prediction Program to Identify the Location of Protein–Protein Binding Sites}, volume={338}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2004.02.040}, DOI={10.1016/j.jmb.2004.02.040}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Neuvirth, Hani and Raz, Ran and Schreiber, Gideon}, year={2004}, month=apr, pages={181–199} }

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    "S0022283604002086"
  ],
  "URL": "http://dx.doi.org/10.1016/j.jmb.2004.02.040",
  "relation": {},
  "ISSN": [
    "0022-2836"
  ],
  "subject": [],
  "container-title-short": "Journal of Molecular Biology",
  "published": {
    "date-parts": [
      [
        2004,
        4
      ]
    ]
  }
}