메뉴 건너뛰기




Volumn 43, Issue W1, 2015, Pages W431-W435

GalaxyPepDock: A protein-peptide docking tool based on interaction similarity and energy optimization

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; COMPUTER MODEL; GALAXYPEPDOCK WEB SERVER; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR DOCKING; PERFORMANCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN STRUCTURE; SOFTWARE; WEB BROWSER; CHEMISTRY; COMPUTER PROGRAM; INTERNET; METABOLISM; PROCEDURES; PROTEIN CONFORMATION;

EID: 84979863225     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv495     Document Type: Article
Times cited : (226)

References (31)
  • 1
    • 49549083915 scopus 로고    scopus 로고
    • Peptide-mediated interactions in biological systems: New discoveries and applications
    • Petsalaki, E. and Russell, R.B. (2008) Peptide-mediated interactions in biological systems: new discoveries and applications. Curr. Opin. Biotechnol., 19, 344-350.
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 344-350
    • Petsalaki, E.1    Russell, R.B.2
  • 2
    • 70849112486 scopus 로고    scopus 로고
    • Cell signaling in space and time: Where proteins come together and when they're apart
    • Scott, J.D. and Pawson, T. (2009) Cell signaling in space and time: where proteins come together and when they're apart. Science, 326, 1220-1224.
    • (2009) Science , vol.326 , pp. 1220-1224
    • Scott, J.D.1    Pawson, T.2
  • 3
    • 0029130168 scopus 로고
    • Identification of a signal for rapid export of proteins from the nucleus
    • Wen, W., Meinkoth, J.L., Tsien, R.Y. and Taylor, S.S. (1995) Identification of a signal for rapid export of proteins from the nucleus. Cell, 82, 463-473.
    • (1995) Cell , vol.82 , pp. 463-473
    • Wen, W.1    Meinkoth, J.L.2    Tsien, R.Y.3    Taylor, S.S.4
  • 5
    • 79952690543 scopus 로고    scopus 로고
    • How phosphorylation controls p53
    • MacLaine, N.J. and Hupp, T.R. (2011) How phosphorylation controls p53. Cell Cycle, 10, 916-921.
    • (2011) Cell Cycle , vol.10 , pp. 916-921
    • MacLaine, N.J.1    Hupp, T.R.2
  • 6
    • 84934436278 scopus 로고    scopus 로고
    • LMP1 TRAFficking activates growth and survival pathways
    • Soni, V., Cahir-McFarland, E. and Kieff, E. (2007) LMP1 TRAFficking activates growth and survival pathways. Adv. Exp. Med. Biol., 597, 173-187.
    • (2007) Adv. Exp. Med. Biol. , vol.597 , pp. 173-187
    • Soni, V.1    Cahir-McFarland, E.2    Kieff, E.3
  • 9
    • 84888294694 scopus 로고    scopus 로고
    • Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions
    • Lavi, A., Ngan, C.H., Movshovitz-Attias, D., Bohnuud, T., Yueh, C., Beglov, D., Schueler-Furman, O. and Kozakov, D. (2013) Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions. Proteins, 81, 2096-2105.
    • (2013) Proteins , vol.81 , pp. 2096-2105
    • Lavi, A.1    Ngan, C.H.2    Movshovitz-Attias, D.3    Bohnuud, T.4    Yueh, C.5    Beglov, D.6    Schueler-Furman, O.7    Kozakov, D.8
  • 10
    • 84918800801 scopus 로고    scopus 로고
    • Predicting peptide binding sites on protein surfaces by clustering chemical interactions
    • Yan, C. and Zou, X. (2015) Predicting peptide binding sites on protein surfaces by clustering chemical interactions. J. Comput. Chem., 36, 49-61.
    • (2015) J. Comput. Chem. , vol.36 , pp. 49-61
    • Yan, C.1    Zou, X.2
  • 12
    • 84874871709 scopus 로고    scopus 로고
    • A unified conformational selection and induced fit approach to protein-peptide docking
    • Trellet, M., Melquiond, A.S. and Bonvin, A.M. (2013) A unified conformational selection and induced fit approach to protein-peptide docking. PloS One, 8, e58769.
    • (2013) PloS One , vol.8 , pp. e58769
    • Trellet, M.1    Melquiond, A.S.2    Bonvin, A.M.3
  • 13
    • 84864419151 scopus 로고    scopus 로고
    • PepSite: Prediction of peptide-binding sites from protein surfaces
    • Trabuco, L.G., Lise, S., Petsalaki, E. and Russell, R.B. (2012) PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res., 40, W423-W427.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W423-W427
    • Trabuco, L.G.1    Lise, S.2    Petsalaki, E.3    Russell, R.B.4
  • 14
    • 84904785968 scopus 로고    scopus 로고
    • PEP-SiteFinder: A tool for the blind identification of peptide binding sites on protein surfaces
    • Saladin, A., Rey, J., Thevenet, P., Zacharias, M., Moroy, G. and Tuffery, P. (2014) PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces. Nucleic Acids Res., 42, W221-W226.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W221-W226
    • Saladin, A.1    Rey, J.2    Thevenet, P.3    Zacharias, M.4    Moroy, G.5    Tuffery, P.6
  • 15
    • 79959981040 scopus 로고    scopus 로고
    • Rosetta FlexPepDock web server-high resolution modeling of peptide-protein interactions
    • London, N., Raveh, B., Cohen, E., Fathi, G. and Schueler-Furman, O. (2011) Rosetta FlexPepDock web server-high resolution modeling of peptide-protein interactions. Nucleic Acids Res., 39, W249-W253.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W249-W253
    • London, N.1    Raveh, B.2    Cohen, E.3    Fathi, G.4    Schueler-Furman, O.5
  • 16
    • 77953573815 scopus 로고    scopus 로고
    • Sub-angstrom modeling of complexes between flexible peptides and globular proteins
    • Raveh, B., London, N. and Schueler-Furman, O. (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins, 78, 2029-2040.
    • (2010) Proteins , vol.78 , pp. 2029-2040
    • Raveh, B.1    London, N.2    Schueler-Furman, O.3
  • 17
    • 79955716232 scopus 로고    scopus 로고
    • Rosetta FlexPepDock ab-initio: Simultaneous folding, docking and refinement of peptides onto their receptors
    • Raveh, B., London, N., Zimmerman, L. and Schueler-Furman, O. (2011) Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PloS One, 6, e18934.
    • (2011) PloS One , vol.6 , pp. e18934
    • Raveh, B.1    London, N.2    Zimmerman, L.3    Schueler-Furman, O.4
  • 18
    • 80053940464 scopus 로고    scopus 로고
    • PepCrawler: A fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors
    • Donsky, E. and Wolfson, H.J. (2011) PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors. Bioinformatics, 27, 2836-2842.
    • (2011) Bioinformatics , vol.27 , pp. 2836-2842
    • Donsky, E.1    Wolfson, H.J.2
  • 19
    • 75849126506 scopus 로고    scopus 로고
    • The structural basis of peptide-protein binding strategies
    • London, N., Movshovitz-Attias, D. and Schueler-Furman, O. (2010) The structural basis of peptide-protein binding strategies. Structure, 18, 188-199.
    • (2010) Structure , vol.18 , pp. 188-199
    • London, N.1    Movshovitz-Attias, D.2    Schueler-Furman, O.3
  • 20
    • 84888851991 scopus 로고    scopus 로고
    • Peptide docking and structure-based characterization of peptide binding: From knowledge to know-how
    • London, N., Raveh, B. and Schueler-Furman, O. (2013) Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Curr. Opin. Struct. Biol., 23, 894-902.
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 894-902
    • London, N.1    Raveh, B.2    Schueler-Furman, O.3
  • 21
    • 84883590772 scopus 로고    scopus 로고
    • GalaxyRefine: Protein structure refinement driven by side-chain repacking
    • Heo, L., Park, H. and Seok, C. (2013) GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Res., 41, W384-W388.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W384-W388
    • Heo, L.1    Park, H.2    Seok, C.3
  • 22
    • 84863783282 scopus 로고    scopus 로고
    • Refinement of unreliable local regions in template-based protein models
    • Park, H. and Seok, C. (2012) Refinement of unreliable local regions in template-based protein models. Proteins, 80, 1974-1986.
    • (2012) Proteins , vol.80 , pp. 1974-1986
    • Park, H.1    Seok, C.2
  • 23
    • 80051556272 scopus 로고    scopus 로고
    • Refinement of protein termini in template-based modeling using conformational space annealing
    • Park, H., Ko, J., Joo, K., Lee, J., Seok, C. and Lee, J. (2011) Refinement of protein termini in template-based modeling using conformational space annealing. Proteins, 79, 2725-2734.
    • (2011) Proteins , vol.79 , pp. 2725-2734
    • Park, H.1    Ko, J.2    Joo, K.3    Lee, J.4    Seok, C.5    Lee, J.6
  • 24
    • 84913555247 scopus 로고    scopus 로고
    • Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments
    • Park, H., Lee, G.R., Heo, L. and Seok, C. (2014) Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments. PloS One, 9, e113811.
    • (2014) PloS One , vol.9 , pp. e113811
    • Park, H.1    Lee, G.R.2    Heo, L.3    Seok, C.4
  • 25
    • 84888289172 scopus 로고    scopus 로고
    • Docking, scoring, and affinity prediction in CAPRI
    • Lensink, M.F. and Wodak, S.J. (2013) Docking, scoring, and affinity prediction in CAPRI. Proteins, 81, 2082-2095.
    • (2013) Proteins , vol.81 , pp. 2082-2095
    • Lensink, M.F.1    Wodak, S.J.2
  • 26
    • 84883454730 scopus 로고    scopus 로고
    • PepBind: A comprehensive database and computational tool for analysis of protein-peptide interactions
    • Das, A.A., Sharma, O.P., Kumar, M.S., Krishna, R. and Mathur, P.P. (2013) PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions. Genomics Proteomics Bioinformatics, 11, 241-246.
    • (2013) Genomics Proteomics Bioinformatics , vol.11 , pp. 241-246
    • Das, A.A.1    Sharma, O.P.2    Kumar, M.S.3    Krishna, R.4    Mathur, P.P.5
  • 27
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 28
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A., 89, 10915-10919.
    • (1992) Proc. Natl. Acad. Sci. U.S.A , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 29
    • 84864461950 scopus 로고    scopus 로고
    • GalaxyWEB server for protein structure prediction and refinement
    • Ko, J., Park, H., Heo, L. and Seok, C. (2012) GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Res., 40, W294-W297.
    • (2012) Nucleic Acids Res. , vol.40 , pp. W294-W297
    • Ko, J.1    Park, H.2    Heo, L.3    Seok, C.4
  • 30
    • 84864828679 scopus 로고    scopus 로고
    • GalaxyTBM: Template-based modeling by building a reliable core and refining unreliable local regions
    • Ko, J., Park, H. and Seok, C. (2012) GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions. BMC Bioinformatics, 13, 198.
    • (2012) BMC Bioinformatics , vol.13 , pp. 198
    • Ko, J.1    Park, H.2    Seok, C.3
  • 31
    • 84913601869 scopus 로고    scopus 로고
    • Prediction of protein structure and interaction by GALAXY protein modeling programs
    • Shin, W.H., Lee, G.R., Heo, L., Lee, H. and Seok, C. (2014) Prediction of protein structure and interaction by GALAXY protein modeling programs. Bio Des., 2, 1-11.
    • (2014) Bio Des. , vol.2 , pp. 1-11
    • Shin, W.H.1    Lee, G.R.2    Heo, L.3    Lee, H.4    Seok, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.