메뉴 건너뛰기




Volumn 22, Issue 4, 2013, Pages 359-366

Toward a "structural BLAST": Using structural relationships to infer function

Author keywords

Machine learning; Protein interaction prediction; Protein interface prediction; Structure function relationship

Indexed keywords

ACCURACY; ALGORITHM; BAYESIAN LEARNING; GENOMICS; LIGAND BINDING; MACHINE LEARNING; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; STRUCTURAL BLAST APPROACH; STRUCTURAL HOMOLOGY;

EID: 84878282902     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2225     Document Type: Review
Times cited : (17)

References (49)
  • 3
    • 77954288774 scopus 로고    scopus 로고
    • Dali server: Conservation mapping in 3D
    • Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38: W545-W549.
    • (2010) Nucleic Acids Res , vol.38
    • Holm, L.1    Rosenström, P.2
  • 4
    • 33744805069 scopus 로고    scopus 로고
    • Protein structure comparison: Implications for the nature of 'fold space', and structure and function prediction
    • DOI 10.1016/j.sbi.2006.04.007, PII S0959440X06000716
    • Kolodny R, Petrey D, Honig B (2006) Protein structure comparison: implications for the nature of 'fold space', and structure and function prediction. Curr Opin Struct Biol 16: 393-398. (Pubitemid 43831645)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.3 , pp. 393-398
    • Kolodny, R.1    Petrey, D.2    Honig, B.3
  • 5
    • 70350465128 scopus 로고    scopus 로고
    • Structural relationships among proteins with different global topologies and their implications for function annotation strategies
    • Petrey D, Fischer M, Honig B (2009) Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci USA 106: 17377-17382.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 17377-17382
    • Petrey, D.1    Fischer, M.2    Honig, B.3
  • 6
    • 66549120787 scopus 로고    scopus 로고
    • Is protein classification necessary? Toward alternative approaches to function annotation
    • Petrey D, Honig B (2009) Is protein classification necessary? Toward alternative approaches to function annotation. Curr Opin Struct Biol 19: 363-368.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 363-368
    • Petrey, D.1    Honig, B.2
  • 7
    • 78651081229 scopus 로고    scopus 로고
    • Structural space of protein- protein interfaces is degenerate, close to complete, and highly connected
    • Gao M, Skolnick J (2010) Structural space of protein- protein interfaces is degenerate, close to complete, and highly connected. Proc Natl Acad Sci 107: 22517-22522.
    • (2010) Proc Natl Acad Sci , vol.107 , pp. 22517-22522
    • Gao, M.1    Skolnick, J.2
  • 9
    • 33646472273 scopus 로고    scopus 로고
    • A tale of two ferredoxins: Sequence similarity and structural differences
    • Krishna SS, Sadreyev RI, Grishin NV (2006) A tale of two ferredoxins: sequence similarity and structural differences. BMC Struct Biol 6: 8.
    • (2006) BMC Struct Biol , vol.6 , pp. 8
    • Krishna, S.S.1    Sadreyev, R.I.2    Grishin, N.V.3
  • 10
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin NV (2001) Fold change in evolution of protein structures. J Struct Biol 134: 167-185.
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 11
    • 44949143819 scopus 로고    scopus 로고
    • Cradleloop barrels and the concept of metafolds in protein classification by natural descent
    • Alva V, Koretke KK, Coles M, Lupas AN (2008) Cradleloop barrels and the concept of metafolds in protein classification by natural descent. Curr Opin Struct Biol 18: 358-365.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 358-365
    • Alva, V.1    Koretke, K.K.2    Coles, M.3    Lupas, A.N.4
  • 13
    • 1842607238 scopus 로고    scopus 로고
    • Secondary structure switching in Cro protein evolution
    • DOI 10.1016/j.str.2004.02.024, PII S0969212604000668
    • Newlove T, Konieczka JH, Cordes MH (2004) Secondary structure switching in Cro protein evolution. Structure 12: 569-581. (Pubitemid 38447160)
    • (2004) Structure , vol.12 , Issue.4 , pp. 569-581
    • Newlove, T.1    Konieczka, J.H.2    Cordes, M.H.J.3
  • 14
    • 33846653633 scopus 로고    scopus 로고
    • Using an alignment of fragment strings for comparing protein structures
    • DOI 10.1093/bioinformatics/btl310
    • Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A (2007) Using an alignment of fragment strings for comparing protein structures. Bioinformatics 23: e219-e224. (Pubitemid 46189660)
    • (2007) Bioinformatics , vol.23 , Issue.2
    • Friedberg, I.1    Harder, T.2    Kolodny, R.3    Sitbon, E.4    Li, Z.5    Godzik, A.6
  • 15
    • 44449139387 scopus 로고    scopus 로고
    • Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
    • DOI 10.1073/pnas.0704422105
    • Xie L, Bourne PE (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci U S A 105: 5441-5446. (Pubitemid 351753882)
    • (2008) Proceedings of the National Academy of Sciences of the United States of America , vol.105 , Issue.14 , pp. 5441-5446
    • Xie, L.1    Bourne, P.E.2
  • 17
    • 36949009488 scopus 로고    scopus 로고
    • In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators
    • Xie L, Wang J, Bourne PE (2007) In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators. PLoS Comp Biol 3: e217.
    • (2007) PLoS Comp Biol , vol.3
    • Xie, L.1    Wang, J.2    Bourne, P.E.3
  • 18
    • 47849091218 scopus 로고    scopus 로고
    • Architectures and functional coverage of protein- protein interfaces
    • Tuncbag N, Gursoy A, Guney E, Nussinov R, Keskin O (2008) Architectures and functional coverage of protein- protein interfaces. J Mol Biol 381: 785-802.
    • (2008) J Mol Biol , vol.381 , pp. 785-802
    • Tuncbag, N.1    Gursoy, A.2    Guney, E.3    Nussinov, R.4    Keskin, O.5
  • 19
    • 80052411919 scopus 로고    scopus 로고
    • Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
    • Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protocols 6: 1341-1354.
    • (2011) Nat Protocols , vol.6 , pp. 1341-1354
    • Tuncbag, N.1    Gursoy, A.2    Nussinov, R.3    Keskin, O.4
  • 22
    • 0242720595 scopus 로고    scopus 로고
    • The PDB is a covering set of small protein structures
    • DOI 10.1016/j.jmb.2003.10.027
    • Kihara D, Skolnick J (2003) The PDB is a covering set of small protein structures. J Mol Biol 334: 793-802. (Pubitemid 37433892)
    • (2003) Journal of Molecular Biology , vol.334 , Issue.4 , pp. 793-802
    • Kihara, D.1    Skolnick, J.2
  • 23
    • 84862276163 scopus 로고    scopus 로고
    • Further evidence for the likely completeness of the library of solved single domain protein structures
    • Skolnick J, Zhou H, Brylinski M (2012) Further evidence for the likely completeness of the library of solved single domain protein structures. J Phys Chem B 116: 6654-6664.
    • (2012) J Phys Chem B , vol.116 , pp. 6654-6664
    • Skolnick, J.1    Zhou, H.2    Brylinski, M.3
  • 24
    • 0142106373 scopus 로고    scopus 로고
    • How well is enzyme function conserved as a function of pairwise sequence identity?
    • DOI 10.1016/j.jmb.2003.08.057
    • Tian W, Skolnick J (2003) How well is enzyme function conserved as a function of pairwise sequence identity? J Mol Biol 333: 863-882. (Pubitemid 37268023)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.4 , pp. 863-882
    • Tian, W.1    Skolnick, J.2
  • 26
    • 0036643477 scopus 로고    scopus 로고
    • Monophyly of Class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: Implications for protein evolution in the RNA world
    • DOI 10.1002/prot.10064
    • Aravind L, Anantharaman V, Koonin EV (2002) Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA world. Proteins 48: 1-14. (Pubitemid 34595044)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.1 , pp. 1-14
    • Aravind, L.1    Anantharaman, V.2    Koonin, E.V.3
  • 27
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • DOI 10.1093/nar/gki524
    • Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309. (Pubitemid 41439897)
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 28
    • 0028871926 scopus 로고
    • Dali: A network tool for protein structure comparison
    • Holm L, Sander C (1995) Dali: a network tool for protein structure comparison. Trends Biochem Sci 20: 478-480.
    • (1995) Trends Biochem Sci , vol.20 , pp. 478-480
    • Holm, L.1    Sander, C.2
  • 29
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
    • DOI 10.1016/j.jmb.2004.12.032
    • Kolodny R, Koehl P, Levitt M (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J Mol Biol 346: 1173-1188. (Pubitemid 40215537)
    • (2005) Journal of Molecular Biology , vol.346 , Issue.4 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3
  • 31
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds. Binding site similarity in the absence of homology
    • DOI 10.1006/jmbi.1998.2043
    • Russell RB, Sasieni PD, Sternberg MJ (1998) Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 282: 903-918. (Pubitemid 28442355)
    • (1998) Journal of Molecular Biology , vol.282 , Issue.4 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.E.3
  • 32
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M, Skolnick J (2008) A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc Natl Acad Sci USA 105: 129-134.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 33
    • 0037110589 scopus 로고    scopus 로고
    • Multiprospector: An algorithm for the prediction of protein-protein interactions by multimeric threading
    • DOI 10.1002/prot.10222
    • Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49: 350-364. (Pubitemid 35231471)
    • (2002) Proteins: Structure, Function and Genetics , vol.49 , Issue.3 , pp. 350-364
    • Lu, L.1    Lu, H.2    Skolnick, J.3
  • 34
    • 0346122798 scopus 로고    scopus 로고
    • GRASP2: Visualization, surface properties, and electrostatics of macromolecular structures and sequences
    • DOI 10.1016/S0076-6879(03)74021-X
    • Petrey D, Honig B (2003) GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods Enzymol 374: 492-509. (Pubitemid 37531822)
    • (2003) Methods in Enzymology , vol.374 , pp. 492-509
    • Petrey, D.1    Honig, B.2
  • 35
    • 0034682881 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
    • Yang AS, Honig B (2000) An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J Mol Biol 301: 665-678.
    • (2000) J Mol Biol , vol.301 , pp. 665-678
    • Yang, A.S.1    Honig, B.2
  • 36
    • 77957944014 scopus 로고    scopus 로고
    • Protein- protein docking benchmark version 4.0
    • Hwang H, Vreven T, Janin J, Weng Z (2010) Protein- protein docking benchmark version 4.0. Proteins 78: 3111-3114.
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 37
    • 79959947610 scopus 로고    scopus 로고
    • PredUs: A web server for predicting protein interfaces using structural neighbors
    • Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D (2011) PredUs: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res 39: W283-W287.
    • (2011) Nucleic Acids Res , vol.39
    • Zhang, Q.C.1    Deng, L.2    Fisher, M.3    Guan, J.4    Honig, B.5    Petrey, D.6
  • 38
    • 38549088882 scopus 로고    scopus 로고
    • LigASite - A database of biologically relevant binding sites in proteins with known apo-structures
    • DOI 10.1093/nar/gkm839
    • Dessailly BH, Lensink MF, Orengo CA, Wodak SJ (2008) LigASite-a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res 36: D667-D673. (Pubitemid 351149804)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Dessailly, B.H.1    Lensink, M.F.2    Orengo, C.A.3    Wodak, S.J.4
  • 41
    • 0842288337 scopus 로고    scopus 로고
    • Inferring cellular networks using probabilistic graphical models
    • DOI 10.1126/science.1094068
    • Friedman N (2004) Inferring cellular networks using probabilistic graphical models. Science 303: 799-805. (Pubitemid 38174650)
    • (2004) Science , vol.303 , Issue.5659 , pp. 799-805
    • Friedman, N.1
  • 44
    • 39149143293 scopus 로고    scopus 로고
    • A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas
    • Mani KM, Lefebvre C, Wang K, Lim WK, Basso K, Dalla-Favera R, Califano A (2008) A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Systems Biol 4: 1-9.
    • (2008) Mol Systems Biol , vol.4 , pp. 1-9
    • Mani, K.M.1    Lefebvre, C.2    Wang, K.3    Lim, W.K.4    Basso, K.5    Dalla-Favera, R.6    Califano, A.7
  • 47
    • 79960164372 scopus 로고    scopus 로고
    • Protein-protein complex structure predictions by multimeric threading and template recombination
    • Mukherjee S, Zhang Y (2011) Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 19: 955-966.
    • (2011) Structure , vol.19 , pp. 955-966
    • Mukherjee, S.1    Zhang, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.