메뉴 건너뛰기




Volumn 5, Issue 9, 2010, Pages 1-8

SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN SH3; PEPTIDE; PROTEIN;

EID: 77958588478     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012654     Document Type: Article
Times cited : (2)

References (29)
  • 1
    • 0037453510 scopus 로고    scopus 로고
    • Assembly of cell regulatory systems through protein interaction domains
    • Pawson T, Nash P (2003) Assembly of cell regulatory systems through protein interaction domains. Science 300: 445-452.
    • (2003) Science , vol.300 , pp. 445-452
    • Pawson, T.1    Nash, P.2
  • 2
    • 0030950608 scopus 로고    scopus 로고
    • Modular peptide recognition domains in eukaryotic signaling
    • Kuriyan J, Cowburn D (1997) Modular peptide recognition domains in eukaryotic signaling. Annu Rev Biophys Biomol Struct 26: 259-288.
    • (1997) Annu Rev Biophys Biomol Struct , vol.26 , pp. 259-288
    • Kuriyan, J.1    Cowburn, D.2
  • 3
    • 0026656122 scopus 로고
    • Spot-Synthesis - an Easy Technique for the Positionally Addressable, Parallel Chemical Synthesis on a Membrane Support
    • Frank R (1992) Spot-Synthesis - an Easy Technique for the Positionally Addressable, Parallel Chemical Synthesis on a Membrane Support. Tetrahedron 48: 9217-9232.
    • (1992) Tetrahedron , vol.48 , pp. 9217-9232
    • Frank, R.1
  • 6
    • 0038219754 scopus 로고    scopus 로고
    • Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides
    • Suenaga A, Hatakeyama M, Ichikawa M, Yu X, Futatsugi N, et al. (2003) Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides. Biochemistry 42: 5195-5200.
    • (2003) Biochemistry , vol.42 , pp. 5195-5200
    • Suenaga, A.1    Hatakeyama, M.2    Ichikawa, M.3    Yu, X.4    Futatsugi, N.5
  • 7
    • 70450065485 scopus 로고    scopus 로고
    • Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior
    • Gerek ZN, Keskin O, Ozkan SB (2009) Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior. Proteins 77: 796-811.
    • (2009) Proteins , vol.77 , pp. 796-811
    • Gerek, Z.N.1    Keskin, O.2    Ozkan, S.B.3
  • 8
    • 0034724569 scopus 로고    scopus 로고
    • SH3- SPOT: An algorithm to predict preferred ligands to different members of the SH3 gene family
    • Brannetti B, Via A, Cestra G, Cesareni G, Helmer-Citterich M (2000) SH3- SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J Mol Biol 298: 313-328.
    • (2000) J Mol Biol , vol.298 , pp. 313-328
    • Brannetti, B.1    Via, A.2    Cestra, G.3    Cesareni, G.4    Helmer-Citterich, M.5
  • 9
    • 0035950043 scopus 로고    scopus 로고
    • Toward the quantitative prediction of T-cell epitopes: CoMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201
    • Doytchinova IA, Flower DR (2001) Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201. J Med Chem 44: 3572-3581.
    • (2001) J Med Chem , vol.44 , pp. 3572-3581
    • Doytchinova, I.A.1    Flower, D.R.2
  • 10
    • 33645776269 scopus 로고    scopus 로고
    • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
    • Hou T, Chen K, McLaughlin WA, Lu B, Wang W (2006) Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol 2: e1.
    • (2006) PLoS Comput Biol , vol.2
    • Hou, T.1    Chen, K.2    McLaughlin, W.A.3    Lu, B.4    Wang, W.5
  • 11
    • 66149146342 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: A generic structurebased model to decipher the binding specificity of SH3 domains
    • Hou T, Xu Z, Zhang W, McLaughlin WA, Case DA, et al. (2009) Characterization of domain-peptide interaction interface: a generic structurebased model to decipher the binding specificity of SH3 domains. Mol Cell Proteomics 8: 639-649.
    • (2009) Mol Cell Proteomics , vol.8 , pp. 639-649
    • Hou, T.1    Xu, Z.2    Zhang, W.3    McLaughlin, W.A.4    Case, D.A.5
  • 12
    • 39049111013 scopus 로고    scopus 로고
    • Characterization of domainpeptide interaction interface: A case study on the amphiphysin-1 SH3 domain
    • Hou TJ, Zhang W, Case DA, Wang W (2008) Characterization of domainpeptide interaction interface: A case study on the amphiphysin-1 SH3 domain. Journal of Molecular Biology 376: 1201-1214.
    • (2008) Journal of Molecular Biology , vol.376 , pp. 1201-1214
    • Hou, T.J.1    Zhang, W.2    Case, D.A.3    Wang, W.4
  • 13
    • 69049083531 scopus 로고    scopus 로고
    • Using genome-wide measurements for computational prediction of SH2-peptide interactions
    • Wunderlich Z, Mirny LA (2009) Using genome-wide measurements for computational prediction of SH2-peptide interactions. Nucleic Acids Res 37: 4629-4641.
    • (2009) Nucleic Acids Res , vol.37 , pp. 4629-4641
    • Wunderlich, Z.1    Mirny, L.A.2
  • 14
    • 12144276041 scopus 로고    scopus 로고
    • Predicting protein-peptide interactions via a network-based motif sampler
    • Reiss DJ, Schwikowski B (2004) Predicting protein-peptide interactions via a network-based motif sampler. Bioinformatics 20(Suppl 1): i274-282.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Reiss, D.J.1    Schwikowski, B.2
  • 15
    • 33644870557 scopus 로고    scopus 로고
    • A regularized discriminative model for the prediction of protein-peptide interactions
    • Lehrach WP, Husmeier D, Williams CK (2006) A regularized discriminative model for the prediction of protein-peptide interactions. Bioinformatics 22: 532-540.
    • (2006) Bioinformatics , vol.22 , pp. 532-540
    • Lehrach, W.P.1    Husmeier, D.2    Williams, C.K.3
  • 16
    • 34250721648 scopus 로고    scopus 로고
    • Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion
    • Hilpert K, Winkler DF, Hancock RE (2007) Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat Protoc 2: 1333-1349.
    • (2007) Nat Protoc , vol.2 , pp. 1333-1349
    • Hilpert, K.1    Winkler, D.F.2    Hancock, R.E.3
  • 18
    • 0032509175 scopus 로고    scopus 로고
    • Exploiting the basis of proline recognition by SH3 and WW domains: Design of N-substituted inhibitors
    • Nguyen JT, Turck CW, Cohen FE, Zuckermann RN, Lim WA (1998) Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science 282: 2088-2092.
    • (1998) Science , vol.282 , pp. 2088-2092
    • Nguyen, J.T.1    Turck, C.W.2    Cohen, F.E.3    Zuckermann, R.N.4    Lim, W.A.5
  • 19
    • 67349248904 scopus 로고    scopus 로고
    • Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions
    • Fernandez-Ballester G, Beltrao P, Gonzalez JM, Song YH, Wilmanns M, et al. (2009) Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions. J Mol Biol 388: 902-916.
    • (2009) J Mol Biol , vol.388 , pp. 902-916
    • Fernandez-Ballester, G.1    Beltrao, P.2    Gonzalez, J.M.3    Song, Y.H.4    Wilmanns, M.5
  • 20
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
    • Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. Journal of Molecular Biology 320: 369-387.
    • (2002) Journal of Molecular Biology , vol.320 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 24
    • 36749031065 scopus 로고    scopus 로고
    • ClusPro: Performance in CAPRI rounds 6-11 and the new server
    • Comeau SR, Kozakov D, Brenke R, Shen Y, Beglov D, et al. (2007) ClusPro: performance in CAPRI rounds 6-11 and the new server. Proteins 69: 781-785.
    • (2007) Proteins , vol.69 , pp. 781-785
    • Comeau, S.R.1    Kozakov, D.2    Brenke, R.3    Shen, Y.4    Beglov, D.5
  • 26
    • 0027136282 scopus 로고
    • Comparative Protein Modeling by Satisfaction of Spatial Restraints
    • Sali A, Blundell TL (1993) Comparative Protein Modeling by Satisfaction of Spatial Restraints. Journal of Molecular Biology 234: 779-815.
    • (1993) Journal of Molecular Biology , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 28
    • 20544435097 scopus 로고    scopus 로고
    • Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
    • Sorin EJ, Pande VS (2005) Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal 88: 2472-2493.
    • (2005) Biophysical Journal , vol.88 , pp. 2472-2493
    • Sorin, E.J.1    Pande, V.S.2
  • 29
    • 0242663237 scopus 로고    scopus 로고
    • A pointcharge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • Duan Y, Wu C, Chowdhury S, Lee MC, Xiong GM, et al. (2003) A pointcharge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24: 1999-2012.
    • (2003) Journal of Computational Chemistry , vol.24 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.