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Volumn 6, Issue 3, 2008, Pages 415-433

PPiClust: Effect clustering of 3D protein-protein interaction interfaces

Author keywords

3D interaction interfaces; Efficient clustering; Protein Protein interaction

Indexed keywords

ACCURACY; CLUSTER ANALYSIS; COMPLEX FORMATION; COMPUTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; CONFERENCE PAPER; PROTEIN ANALYSIS; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STATISTICAL SIGNIFICANCE; ARTICLE; CHEMISTRY; PHYSIOLOGY; PROTEIN BINDING; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

EID: 46049099795     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003485     Document Type: Conference Paper
Times cited : (9)

References (32)
  • 2
    • 0038620469 scopus 로고    scopus 로고
    • Integrative approach for computationally inferring protein domain interactions
    • Ng SK, Zhang Z, Tan SH, Integrative approach for computationally inferring protein domain interactions, Bioinformatics 19 923-929, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 923-929
    • Ng, S.K.1    Zhang, Z.2    Tan, S.H.3
  • 3
    • 20444414545 scopus 로고    scopus 로고
    • Linear motifs: Evolutionary interaction switches
    • Neduva V, Russell RB, Linear motifs: Evolutionary interaction switches, FEBS Lett 579:3342-3345, 2005.
    • (2005) FEBS Lett , vol.579 , pp. 3342-3345
    • Neduva, V.1    Russell, R.B.2
  • 4
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J, The atomic structure of protein-protein recognition sites, J Mol Biol 285:2177-2198, 1999.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 5
    • 0034213559 scopus 로고    scopus 로고
    • Conservation of polar residues as hot spots at protein interfaces
    • Hu Z, Ma B, Wolfson H, Nussinov R, Conservation of polar residues as hot spots at protein interfaces, Proteins 39:331-342, 2000.
    • (2000) Proteins , vol.39 , pp. 331-342
    • Hu, Z.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 6
    • 33646553913 scopus 로고    scopus 로고
    • SCOWLP: A web-based database for detailed characterization and visualization of protein interfaces
    • Teyra J, Doms A, Schroeder M, Pisabarro MT, SCOWLP: A web-based database for detailed characterization and visualization of protein interfaces, BMC Bioinformatics 7:104, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 104
    • Teyra, J.1    Doms, A.2    Schroeder, M.3    Pisabarro, M.T.4
  • 7
    • 0030602896 scopus 로고    scopus 로고
    • A dataset of protein-protein interfaces generated with sequence-order-independent comparison technique
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R, A dataset of protein-protein interfaces generated with sequence-order-independent comparison technique, J Mol Biol 260:604-620, 1996.
    • (1996) J Mol Biol , vol.260 , pp. 604-620
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 8
    • 1842507022 scopus 로고    scopus 로고
    • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications
    • Keskin O, Tsai CJ, Wolfson H, Nussinov R, A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications, Protein Sci 13:1043-1055, 2004.
    • (2004) Protein Sci , vol.13 , pp. 1043-1055
    • Keskin, O.1    Tsai, C.J.2    Wolfson, H.3    Nussinov, R.4
  • 9
    • 24344487344 scopus 로고    scopus 로고
    • Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    • Mintz S, Shulman-Peleg A, Wolfson HJ, Nussinov R, Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions, Proteins 61:6-20, 2005.
    • (2005) Proteins , vol.61 , pp. 6-20
    • Mintz, S.1    Shulman-Peleg, A.2    Wolfson, H.J.3    Nussinov, R.4
  • 10
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: A comprehensive database of structurally defined protein interfaces
    • Davis FP, Sali A, PIBASE: A comprehensive database of structurally defined protein interfaces, Bioinformatics 21:1901-1907, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 11
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • Handl J, Knowles J, Kell DB, Computational cluster validation in post-genomic data analysis, Bioinformatics 21:3201-3212, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 3201-3212
    • Handl, J.1    Knowles, J.2    Kell, D.B.3
  • 12
    • 46049116954 scopus 로고    scopus 로고
    • personal communication
    • Shulman-Peleg A, personal communication, 2005.
    • (2005)
    • Shulman-Peleg, A.1
  • 13
    • 2442614144 scopus 로고    scopus 로고
    • Recognition of functional sites in protein structures
    • Shulman-Peleg A, Nussinov R, Wolfson HJ, Recognition of functional sites in protein structures, J Mol Biol 339:607-633, 2004.
    • (2004) J Mol Biol , vol.339 , pp. 607-633
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 15
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C, Protein structure comparison by alignment of distance matrices, J Mol Biol 233:123-138, 1993.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 16
    • 0035419858 scopus 로고    scopus 로고
    • Content based image retrieval and information theory: A general approach
    • Zachary J, Iyengar SS, Baxhen J, Content based image retrieval and information theory: A general approach, J Am Soc Inf Sci Technol 52:840-852, 2001.
    • (2001) J Am Soc Inf Sci Technol , vol.52 , pp. 840-852
    • Zachary, J.1    Iyengar, S.S.2    Baxhen, J.3
  • 17
    • 0036304230 scopus 로고    scopus 로고
    • Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison
    • Caxugo O, Pongor S, Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison, J Mol Biol 315:887-898, 2002.
    • (2002) J Mol Biol , vol.315 , pp. 887-898
    • Caxugo, O.1    Pongor, S.2
  • 18
    • 1642389927 scopus 로고    scopus 로고
    • Local feature frequency profile: A method to measure structural similarity in proteins
    • Choi IG, Kwon J, Kim SH, Local feature frequency profile: A method to measure structural similarity in proteins, Proc Natl Acad Sci USA 101:3797-3802, 2004.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3797-3802
    • Choi, I.G.1    Kwon, J.2    Kim, S.H.3
  • 22
    • 46049120903 scopus 로고    scopus 로고
    • http://www.unesco.org/webworld/idams/advguide/Chapt7_1_l.htm/.
  • 23
    • 84856043672 scopus 로고
    • A mathematical theory of communication
    • Shannon CE, A mathematical theory of communication, Bell Syst Tech J 27:379-423, 1948.
    • (1948) Bell Syst Tech J , vol.27 , pp. 379-423
    • Shannon, C.E.1
  • 24
    • 9144244232 scopus 로고    scopus 로고
    • MODBASE, a database of annotated comparative protein structure models, and associated resources
    • Pieper U, Eswar N, Braberg H et al., MODBASE, a database of annotated comparative protein structure models, and associated resources, Nucleic Acids Res 32:D217-D222, 2004.
    • (2004) Nucleic Acids Res , vol.32
    • Pieper, U.1    Eswar, N.2    Braberg, H.3
  • 25
    • 0030768266 scopus 로고    scopus 로고
    • Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes
    • Tsai CJ, Xu D, Nussinov R, Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes, Protein Sci 6:1793-1805, 1997.
    • (1997) Protein Sci , vol.6 , pp. 1793-1805
    • Tsai, C.J.1    Xu, D.2    Nussinov, R.3
  • 26
    • 13844255392 scopus 로고    scopus 로고
    • Protein complexes: Structure prediction challenges for the 21st century
    • Aloy P, Pichaud M, Russell RB, Protein complexes: Structure prediction challenges for the 21st century, Curr Opin Struct Biol 15 15-22, 2005.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 15-22
    • Aloy, P.1    Pichaud, M.2    Russell, R.B.3
  • 28
    • 0042622252 scopus 로고    scopus 로고
    • A new resource for investigating short functional sites in modular eukaryotic proteins
    • ELM server
    • Puntervoll P, Linding R, Gemund C et al., ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins, Nucleic Acids Res 31:3625-3630, 2003.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3625-3630
    • Puntervoll, P.1    Linding, R.2    Gemund, C.3
  • 29
    • 0037076540 scopus 로고    scopus 로고
    • Common alpha-helical interaction motifs in proteins, particularly in extremophiles
    • GXXXG and AXXXA
    • Kleiger G, Grothe R, Mallick P, Eisenberg D, GXXXG and AXXXA: Common alpha-helical interaction motifs in proteins, particularly in extremophiles, Biochemistry 41:5990-5997, 2002.
    • (2002) Biochemistry , vol.41 , pp. 5990-5997
    • Kleiger, G.1    Grothe, R.2    Mallick, P.3    Eisenberg, D.4
  • 31
    • 10344226713 scopus 로고    scopus 로고
    • Parasitology: The malarial secretome
    • Przyborski J, Lanzer M, Parasitology: The malarial secretome, Science 306:1897-1898, 2004.
    • (2004) Science , vol.306 , pp. 1897-1898
    • Przyborski, J.1    Lanzer, M.2
  • 32
    • 1842815895 scopus 로고    scopus 로고
    • Distribution of proline-rich (PxxP) motifs in distinct proteornes: Functional and therapeutic implications for malaria and tuberculosis
    • Ravi Chandra B, Gowthaman R, Raj Akhouri R, Gupta D, Sharma A, Distribution of proline-rich (PxxP) motifs in distinct proteornes: Functional and therapeutic implications for malaria and tuberculosis, Protein Eng Des Sel 17:175-182, 2004.
    • (2004) Protein Eng Des Sel , vol.17 , pp. 175-182
    • Ravi Chandra, B.1    Gowthaman, R.2    Raj Akhouri, R.3    Gupta, D.4    Sharma, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.