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Volumn 13, Issue 1, 2012, Pages

A resource for benchmarking the usefulness of protein structure models

Author keywords

Comparative modeling; Decoy database; ModelDB; Protein structure prediction

Indexed keywords

BIOPERL; COMPARATIVE MODELING; COMPUTATIONAL EXPERIMENT; COMPUTATIONAL TOOLS; DESIGN EXPERIMENTS; JAVA RUNTIME ENVIRONMENTS; JAVASCRIPT; MODELDB; NON-REDUNDANT; PLATFORM INDEPENDENT; PROTEIN STRUCTURE PREDICTION; PROTEIN STRUCTURES; STRUCTURE-BASED; THREE-DIMENSIONAL STRUCTURE; WEB SERVERS;

EID: 84864451829     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-188     Document Type: Article
Times cited : (2)

References (29)
  • 2
    • 0029916911 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence data bank and its new supplement TrEMBL
    • 10.1093/nar/24.1.21, 145613, 8594581
    • Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TrEMBL. Nucleic Acids Res 1996, 24:21-5. 10.1093/nar/24.1.21, 145613, 8594581.
    • (1996) Nucleic Acids Res , vol.24 , pp. 21-25
    • Bairoch, A.1    Apweiler, R.2
  • 3
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • 1166865, 3709526
    • Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986, 5:823-6. 1166865, 3709526.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 4
    • 84995046262 scopus 로고
    • A large-scale experiment to assess protein structure prediction methods
    • 10.1002/prot.340230303, 8710822
    • Moult J, Pedersen JT, Judson R, Fidelis K. A large-scale experiment to assess protein structure prediction methods. Proteins 1995, 23:ii-v. 10.1002/prot.340230303, 8710822.
    • (1995) Proteins , vol.23
    • Moult, J.1    Pedersen, J.T.2    Judson, R.3    Fidelis, K.4
  • 5
    • 80855131663 scopus 로고    scopus 로고
    • Evaluation of model quality predictions in CASP9
    • Kryshtafovych A, Fidelis K, Tramontano A. Evaluation of model quality predictions in CASP9. Proteins 2011, 79(Suppl 10):91-106.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 91-106
    • Kryshtafovych, A.1    Fidelis, K.2    Tramontano, A.3
  • 6
    • 2442677781 scopus 로고    scopus 로고
    • Large-scale assessment of the utility of lowresolution protein structures for biochemical function assignment
    • 10.1093/bioinformatics/bth044, 14764543
    • Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of lowresolution protein structures for biochemical function assignment. Bioinformatics 2004, 20:1087-96. 10.1093/bioinformatics/bth044, 14764543.
    • (2004) Bioinformatics , vol.20 , pp. 1087-1096
    • Arakaki, A.K.1    Zhang, Y.2    Skolnick, J.3
  • 7
    • 36348992229 scopus 로고    scopus 로고
    • Modeling and analyzing three-dimensional structures of human disease proteins
    • Hawaii, Altman RB, Murray T, 3035241, 21304668
    • Ye Y, Li Z, Godzik A. Modeling and analyzing three-dimensional structures of human disease proteins. Proceedings of the Pacific Symposium on Biocomputing: 3-7 January 2006 439-450. Hawaii, Altman RB, Murray T, http://psb.stanford.edu/psb-online/proceedings/psb06/, 3035241, 21304668.
    • Proceedings of the Pacific Symposium on Biocomputing: 3-7 January 2006 , pp. 439-450
    • Ye, Y.1    Li, Z.2    Godzik, A.3
  • 8
    • 46449128188 scopus 로고    scopus 로고
    • Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints
    • 10.1002/jcc.20917, 2726574, 18293308
    • Brylinski M, Skolnick J. Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J Comput Chem 2008, 29:1574-88. 10.1002/jcc.20917, 2726574, 18293308.
    • (2008) J Comput Chem , vol.29 , pp. 1574-1588
    • Brylinski, M.1    Skolnick, J.2
  • 9
    • 33846202561 scopus 로고    scopus 로고
    • Automatic procedure for using models of proteins in molecular replacement
    • Raimondo D, Giorgetti A, Bosi S, Tramontano A. Automatic procedure for using models of proteins in molecular replacement. Proteins 2007, 66:689-96.
    • (2007) Proteins , vol.66 , pp. 689-696
    • Raimondo, D.1    Giorgetti, A.2    Bosi, S.3    Tramontano, A.4
  • 10
    • 27544504227 scopus 로고    scopus 로고
    • Evaluating the usefulness of protein structure models for molecular replacement
    • 10.1093/bioinformatics/bti1112, 16204129
    • Giorgetti A, Raimondo D, Miele AE, Tramontano A. Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics 2005, 21(Suppl 2):ii72-ii76. 10.1093/bioinformatics/bti1112, 16204129.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Giorgetti, A.1    Raimondo, D.2    Miele, A.E.3    Tramontano, A.4
  • 11
    • 34548319111 scopus 로고    scopus 로고
    • In silico pharmacology for drug discovery: applications to targets and beyond
    • 10.1038/sj.bjp.0707306, 1978280, 17549046
    • Ekins S, Mestres J, Testa B. In silico pharmacology for drug discovery: applications to targets and beyond. Br J Pharmacol 2007, 152:21-37. 10.1038/sj.bjp.0707306, 1978280, 17549046.
    • (2007) Br J Pharmacol , vol.152 , pp. 21-37
    • Ekins, S.1    Mestres, J.2    Testa, B.3
  • 13
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • 10.1093/bioinformatics/btg224, 12912846
    • Wang G, Dunbrack RL. PISCES: a protein sequence culling server. Bioinformatics 2003, 19:1589-91. 10.1093/bioinformatics/btg224, 12912846.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, R.L.2
  • 14
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • 1160169, 15980461
    • Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005, 33(Web Server issue):W244-W248. 1160169, 15980461.
    • (2005) Nucleic Acids Res , vol.33 , Issue.WEB SERVER ISSUE
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 17
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • 10.1006/jmbi.1993.1626, 8254673
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815. 10.1006/jmbi.1993.1626, 8254673.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 18
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • 10.1110/ps.9.9.1753, 2144714, 11045621
    • Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci 2000, 9:1753-73. 10.1110/ps.9.9.1753, 2144714, 11045621.
    • (2000) Protein Sci , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 19
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • 10.1093/nar/gkg571, 168977, 12824330
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003, 31:3370-4. 10.1093/nar/gkg571, 168977, 12824330.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 20
    • 58149092163 scopus 로고    scopus 로고
    • CREDO: a protein-ligand interaction database for drug discovery
    • 10.1111/j.1747-0285.2008.00762.x, 19207418
    • Schreyer A, Blundell T. CREDO: a protein-ligand interaction database for drug discovery. Chem Biol Drug Des 2009, 73:157-67. 10.1111/j.1747-0285.2008.00762.x, 19207418.
    • (2009) Chem Biol Drug Des , vol.73 , pp. 157-167
    • Schreyer, A.1    Blundell, T.2
  • 21
    • 0036435882 scopus 로고    scopus 로고
    • Analysis of catalytic residues in enzyme active sites
    • 10.1016/S0022-2836(02)01036-7, 12421562
    • Bartlett GJ, Porter CT, Borkakoti N, Thornton JM. Analysis of catalytic residues in enzyme active sites. J Mol Biol 2002, 324:105-21. 10.1016/S0022-2836(02)01036-7, 12421562.
    • (2002) J Mol Biol , vol.324 , pp. 105-121
    • Bartlett, G.J.1    Porter, C.T.2    Borkakoti, N.3    Thornton, J.M.4
  • 22
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • 308762, 14681376
    • Porter CT, Bartlett GJ, Thornton JM. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 2004, 32(Database issue):D129-D133. 308762, 14681376.
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • 10.1002/bip.360221211, 6667333
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-637. 10.1002/bip.360221211, 6667333.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 24
    • 0028881975 scopus 로고
    • SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • 307-8, 10.1016/0263-7855(95)00073-9, 8603061
    • Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13:323-330. 307-8, 10.1016/0263-7855(95)00073-9, 8603061.
    • (1995) J Mol Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 25
    • 43249104982 scopus 로고    scopus 로고
    • PSAIA - protein structure and interaction analyzer
    • 10.1186/1472-6807-8-21, 2364630, 18400099
    • Mihel J, Sikić M, Tomić S, Jeren B, Vlahovicek K. PSAIA - protein structure and interaction analyzer. BMC Struct Biol 2008, 8:21. 10.1186/1472-6807-8-21, 2364630, 18400099.
    • (2008) BMC Struct Biol , vol.8 , pp. 21
    • Mihel, J.1    Sikić, M.2    Tomić, S.3    Jeren, B.4    Vlahovicek, K.5
  • 26
    • 0242458482 scopus 로고    scopus 로고
    • Protein disorder prediction: implications for structural proteomics
    • 10.1016/j.str.2003.10.002, 14604535
    • Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, Russell RB. Protein disorder prediction: implications for structural proteomics. Structure 2003, 11:1453-9. 10.1016/j.str.2003.10.002, 14604535.
    • (2003) Structure , vol.11 , pp. 1453-1459
    • Linding, R.1    Jensen, L.J.2    Diella, F.3    Bork, P.4    Gibson, T.J.5    Russell, R.B.6
  • 27
    • 57049150788 scopus 로고    scopus 로고
    • The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
    • 2686473, 18971256
    • Goldenberg O, Erez E, Nimrod G, Ben-Tal N. The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures. Nucleic Acids Res 2009, 37(Database issue):D323-D327. 2686473, 18971256.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE
    • Goldenberg, O.1    Erez, E.2    Nimrod, G.3    Ben-Tal, N.4
  • 28
    • 0023645203 scopus 로고
    • Interior and surface of monomeric proteins
    • 10.1016/0022-2836(87)90038-6, 3681970
    • Miller S, Janin J, Lesk AM, Chothia C. Interior and surface of monomeric proteins. J Mol Biol 1987, 196:641-56. 10.1016/0022-2836(87)90038-6, 3681970.
    • (1987) J Mol Biol , vol.196 , pp. 641-656
    • Miller, S.1    Janin, J.2    Lesk, A.M.3    Chothia, C.4
  • 29
    • 0020491251 scopus 로고
    • A geometric approach to macromolecule-ligand interactions
    • 10.1016/0022-2836(82)90153-X, 7154081
    • Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982, 161:269-88. 10.1016/0022-2836(82)90153-X, 7154081.
    • (1982) J Mol Biol , vol.161 , pp. 269-288
    • Kuntz, I.D.1    Blaney, J.M.2    Oatley, S.J.3    Langridge, R.4    Ferrin, T.E.5


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