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Volumn 15, Issue 1, 2014, Pages

Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; PROTEIN; WATER;

EID: 84894775341     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-57     Document Type: Article
Times cited : (10)

References (36)
  • 1
    • 84888844161 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • 10.1016/j.sbi.2013.08.003, 23993666
    • Schreiber G, Fleishman SJ. Computational design of protein-protein interactions. Curr Opin Struct Biol 2013, 23(6):903-910. 10.1016/j.sbi.2013.08.003, 23993666.
    • (2013) Curr Opin Struct Biol , vol.23 , Issue.6 , pp. 903-910
    • Schreiber, G.1    Fleishman, S.J.2
  • 2
    • 0026350498 scopus 로고
    • Systematic mutational analyses of protein-protein interfaces
    • Wells J. Systematic mutational analyses of protein-protein interfaces. Methods Enzymol 1991, 202:390-411.
    • (1991) Methods Enzymol , vol.202 , pp. 390-411
    • Wells, J.1
  • 3
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • 10.1006/jmbi.1998.1843, 9653027
    • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280:1-9. 10.1006/jmbi.1998.1843, 9653027.
    • (1998) J Mol Biol , vol.280 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 5
    • 33644878621 scopus 로고    scopus 로고
    • PINT: protein-protein interactions thermodynamic database
    • 1347380, 16381844
    • Kumar MDS, Gromiha MM. PINT: protein-protein interactions thermodynamic database. Nucleic Acids Res 2006, 34(suppl 1):D195-D198. 1347380, 16381844.
    • (2006) Nucleic Acids Res , vol.34 , Issue.SUPPL. 1
    • Kumar, M.D.S.1    Gromiha, M.M.2
  • 6
    • 84870409536 scopus 로고    scopus 로고
    • SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
    • 10.1093/bioinformatics/bts489, 22859501
    • Moal IH, Fernandez-Recio J. SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models. Bioinformatics 2012, 28(20):2600-2607. 10.1093/bioinformatics/bts489, 22859501.
    • (2012) Bioinformatics , vol.28 , Issue.20 , pp. 2600-2607
    • Moal, I.H.1    Fernandez-Recio, J.2
  • 7
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • 10.1126/science.7529940, 7529940
    • Clackson T, Wells J. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267:383-386. 10.1126/science.7529940, 7529940.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Wells, J.2
  • 8
    • 0035066602 scopus 로고    scopus 로고
    • ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions
    • 10.1093/bioinformatics/17.3.284, 11294795
    • Thorn KS, Bogan AA. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001, 17(3):284-285. 10.1093/bioinformatics/17.3.284, 11294795.
    • (2001) Bioinformatics , vol.17 , Issue.3 , pp. 284-285
    • Thorn, K.S.1    Bogan, A.A.2
  • 9
    • 0036291145 scopus 로고    scopus 로고
    • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations
    • 10.1016/S0022-2836(02)00442-4, 12079393
    • Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002, 320(2):369-387. 10.1016/S0022-2836(02)00442-4, 12079393.
    • (2002) J Mol Biol , vol.320 , Issue.2 , pp. 369-387
    • Guerois, R.1    Nielsen, J.E.2    Serrano, L.3
  • 11
    • 0037195144 scopus 로고    scopus 로고
    • A simple physical model for binding energy hot spots in protein-protein complexes
    • 10.1073/pnas.202485799, 137846, 12381794
    • Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002, 99(22):14116-14121. 10.1073/pnas.202485799, 137846, 12381794.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.22 , pp. 14116-14121
    • Kortemme, T.1    Baker, D.2
  • 12
    • 3242879771 scopus 로고    scopus 로고
    • Computational alanine scanning of protein-protein interfaces
    • Kortemme T, Kim DE, Baker D. Computational alanine scanning of protein-protein interfaces. Sci STKE 2004, 2004(219):pl2.
    • (2004) Sci STKE , vol.2004 , Issue.219
    • Kortemme, T.1    Kim, D.E.2    Baker, D.3
  • 13
    • 58149247893 scopus 로고    scopus 로고
    • Predicting free energy changes using structural ensembles
    • 10.1038/nmeth0109-3, 19116609
    • Benedix A, Becker CM, de Groot BL, Caflisch A, Bockmann RA. Predicting free energy changes using structural ensembles. Nat Methods 2009, 6:3-4. 10.1038/nmeth0109-3, 19116609.
    • (2009) Nat Methods , vol.6 , pp. 3-4
    • Benedix, A.1    Becker, C.M.2    de Groot, B.L.3    Caflisch, A.4    Bockmann, R.A.5
  • 14
    • 65849158839 scopus 로고    scopus 로고
    • A feature-based approach to modeling protein-protein interaction hot spots
    • 10.1093/nar/gkp132, 2677884, 19273533
    • Cho KI, Kim D, Lee D. A feature-based approach to modeling protein-protein interaction hot spots. Nucl Acids Res 2009, 37(8):2672-2687. 10.1093/nar/gkp132, 2677884, 19273533.
    • (2009) Nucl Acids Res , vol.37 , Issue.8 , pp. 2672-2687
    • Cho, K.I.1    Kim, D.2    Lee, D.3
  • 15
    • 84880667308 scopus 로고    scopus 로고
    • Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences
    • Chen P, Li J, Wong L, Kuwahara H, Huang J, Gao X. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins: Struct Funct Bioinformatics 2013, 81(8):1351-1362.
    • (2013) Proteins: Struct Funct Bioinformatics , vol.81 , Issue.8 , pp. 1351-1362
    • Chen, P.1    Li, J.2    Wong, L.3    Kuwahara, H.4    Huang, J.5    Gao, X.6
  • 16
    • 34547573955 scopus 로고    scopus 로고
    • Protein-protein interaction hotspots carved into sequences
    • 10.1371/journal.pcbi.0030119, 1914369, 17630824
    • Ofran Y, Rost B. Protein-protein interaction hotspots carved into sequences. PLoS Comput Biol 2007, 3(7):e119. 10.1371/journal.pcbi.0030119, 1914369, 17630824.
    • (2007) PLoS Comput Biol , vol.3 , Issue.7
    • Ofran, Y.1    Rost, B.2
  • 17
    • 55649090573 scopus 로고    scopus 로고
    • Identification of hot-spot residues in protein-protein interactions by computational docking
    • 10.1186/1471-2105-9-447, 2579439, 18939967
    • Grosdidier S, Recio JF. Identification of hot-spot residues in protein-protein interactions by computational docking. BMC Bioinformatics 2008, 9:447. 10.1186/1471-2105-9-447, 2579439, 18939967.
    • (2008) BMC Bioinformatics , vol.9 , pp. 447
    • Grosdidier, S.1    Recio, J.F.2
  • 19
    • 38549092067 scopus 로고    scopus 로고
    • HotSprint: database of computational hot spots in protein interfaces
    • Database-Issue
    • Guney E, Tuncbag N, Keskin O, Gürsoy A. HotSprint: database of computational hot spots in protein interfaces. Nucl Acids Res 2008, 36(Database-Issue):662-666.
    • (2008) Nucl Acids Res , vol.36 , pp. 662-666
    • Guney, E.1    Tuncbag, N.2    Keskin, O.3    Gürsoy, A.4
  • 20
    • 66349094681 scopus 로고    scopus 로고
    • Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
    • 10.1093/bioinformatics/btp240, 19357097
    • Tuncbag N, Gursoy A, Keskin O. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 2009, 25(12):1513-1520. 10.1093/bioinformatics/btp240, 19357097.
    • (2009) Bioinformatics , vol.25 , Issue.12 , pp. 1513-1520
    • Tuncbag, N.1    Gursoy, A.2    Keskin, O.3
  • 21
    • 77951273638 scopus 로고    scopus 로고
    • PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces
    • 10.1093/nar/gkp1158, 2847225, 20008102
    • Assi SA, Tanaka T, Rabbitts TH, Fernandez-Fuentes N. PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucl Acids Res 2010, 38(6):e86. 10.1093/nar/gkp1158, 2847225, 20008102.
    • (2010) Nucl Acids Res , vol.38 , Issue.6
    • Assi, S.A.1    Tanaka, T.2    Rabbitts, T.H.3    Fernandez-Fuentes, N.4
  • 23
    • 84875509029 scopus 로고    scopus 로고
    • Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties
    • Springer: Berlin, Heidelberg, Deng M, Jiang R, Sun F, Zhang X
    • Deng L, Guan J, Wei X, Yi Y, Zhou S. Boosting prediction performance of protein-protein interaction hot spots by using structural neighborhood properties. Research in Computational Molecular Biology, Volume 7821 of Lecture Notes in Computer Science 2013, 333-344. Springer: Berlin, Heidelberg, Deng M, Jiang R, Sun F, Zhang X.
    • (2013) Research in Computational Molecular Biology, Volume 7821 of Lecture Notes in Computer Science , pp. 333-344
    • Deng, L.1    Guan, J.2    Wei, X.3    Yi, Y.4    Zhou, S.5
  • 24
    • 84863285682 scopus 로고    scopus 로고
    • Prediction of hot spots in protein interfaces using a random forest model with hybrid features
    • Wang L, Liu ZP, Zhang XS, Chen L. Prediction of hot spots in protein interfaces using a random forest model with hybrid features. Protein Eng Design Sel 2012, 25(3):119-126.
    • (2012) Protein Eng Design Sel , vol.25 , Issue.3 , pp. 119-126
    • Wang, L.1    Liu, Z.P.2    Zhang, X.S.3    Chen, L.4
  • 25
    • 84883574360 scopus 로고    scopus 로고
    • BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations
    • Web Server issue, 3692068, 23723246
    • Dehouck Y, Kwasigroch JM, Rooman M, Gilis D. BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res 2013, 41(Web Server issue):W333-W339. 3692068, 23723246.
    • (2013) Nucleic Acids Res , vol.41
    • Dehouck, Y.1    Kwasigroch, J.M.2    Rooman, M.3    Gilis, D.4
  • 28
    • 84876435567 scopus 로고    scopus 로고
    • Beta atomic contacts: identifying critical specific contacts in protein binding interfaces
    • 10.1371/journal.pone.0059737, 3632532, 23630569
    • Liu Q, Kwoh CK, Hoi SCH. Beta atomic contacts: identifying critical specific contacts in protein binding interfaces. PLoS ONE 2013, 8(4):e59737. 10.1371/journal.pone.0059737, 3632532, 23630569.
    • (2013) PLoS ONE , vol.8 , Issue.4
    • Liu, Q.1    Kwoh, C.K.2    Hoi, S.C.H.3
  • 29
    • 84888606432 scopus 로고    scopus 로고
    • Binding affinity prediction for protein-ligand complexes based on β contacts and B factor
    • 10.1021/ci400450h, 24191692
    • Liu Q, Kwoh CK, Li J. Binding affinity prediction for protein-ligand complexes based on β contacts and B factor. J Chem Inf Model 2013, 53(11):3076-3085. 10.1021/ci400450h, 24191692.
    • (2013) J Chem Inf Model , vol.53 , Issue.11 , pp. 3076-3085
    • Liu, Q.1    Kwoh, C.K.2    Li, J.3
  • 30
    • 0003742069 scopus 로고    scopus 로고
    • 'NACCESS', computer program
    • Tech. rep., Department of Biochemistry Molecular Biology, University College London, 1993
    • Hubbard SJ, Thornton JM. 'NACCESS', computer program. Tech. rep., Department of Biochemistry Molecular Biology, University College London, 1993.
    • Hubbard, S.J.1    Thornton, J.M.2
  • 32
    • 0242299207 scopus 로고    scopus 로고
    • Atomic contact vectors in protein-protein recognition
    • 10.1002/prot.10432, 14579354
    • Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003, 53(3):629-639. 10.1002/prot.10432, 14579354.
    • (2003) Proteins , vol.53 , Issue.3 , pp. 629-639
    • Mintseris, J.1    Weng, Z.2
  • 33
    • 62549102939 scopus 로고    scopus 로고
    • 'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces
    • 10.1093/bioinformatics/btp058, 2654803, 19179356
    • Li J, Liu Q. 'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces. Bioinformatics 2009, 25(6):743-750. 10.1093/bioinformatics/btp058, 2654803, 19179356.
    • (2009) Bioinformatics , vol.25 , Issue.6 , pp. 743-750
    • Li, J.1    Liu, Q.2
  • 35
    • 77950651626 scopus 로고    scopus 로고
    • APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
    • 10.1186/1471-2105-11-174, 2874803, 20377884
    • Xia JF, Zhao XM, Song J, Huang DS. APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinformatics 2010, 11:174. 10.1186/1471-2105-11-174, 2874803, 20377884.
    • (2010) BMC Bioinformatics , vol.11 , pp. 174
    • Xia, J.F.1    Zhao, X.M.2    Song, J.3    Huang, D.S.4
  • 36
    • 80051576392 scopus 로고    scopus 로고
    • KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features
    • 10.1002/prot.23094, 21735484
    • Zhu X, Mitchell JC. KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density and plasticity features. Proteins 2011, 79(9):2671-2683. 10.1002/prot.23094, 21735484.
    • (2011) Proteins , vol.79 , Issue.9 , pp. 2671-2683
    • Zhu, X.1    Mitchell, J.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.