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Volumn 9, Issue , 2008, Pages

I-TASSER server for protein 3D structure prediction

Author keywords

[No Author keywords available]

Indexed keywords

3-DIMENSIONAL PROTEIN STRUCTURES; CORRELATION COEFFICIENT; FALSE POSITIVE AND FALSE NEGATIVES; OBJECTIVE ASSESSMENT; PROTEIN 3-D STRUCTURE; PROTEIN STRUCTURE PREDICTION; QUANTITATIVE ASSESSMENTS; STRUCTURAL SIMILARITY;

EID: 39449115394     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-40     Document Type: Article
Times cited : (4276)

References (34)
  • 1
    • 0035747811 scopus 로고    scopus 로고
    • CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4
    • 10.1002/prot.10037 11835484
    • Murzin AG Bateman A CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4 Proteins 2001, (Suppl 5):76-85. 10.1002/prot.10037 11835484
    • (2001) Proteins , Issue.SUPPL. 5 , pp. 76-85
    • Murzin, A.G.1    Bateman, A.2
  • 2
    • 0242267511 scopus 로고    scopus 로고
    • Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment
    • 10.1002/prot.10548 14579329
    • Ginalski K Rychlewski L Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment Proteins 2003, 53(Suppl 6):410-417. 10.1002/prot.10548 14579329
    • (2003) Proteins , vol.53 , Issue.SUPPL. 6 , pp. 410-417
    • Ginalski, K.1    Rychlewski, L.2
  • 3
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • 10.1126/science.1065659 11588250
    • Baker D Sali A Protein structure prediction and structural genomics Science 2001, 294(5540):93-96. 10.1126/science.1065659 11588250
    • (2001) Science , vol.294 , Issue.5540 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 4
    • 0034060287 scopus 로고    scopus 로고
    • Structural genomics and its importance for gene function analysis
    • 10.1038/73723 10700142
    • Skolnick J Fetrow JS Kolinski A Structural genomics and its importance for gene function analysis Nat Biotechnol 2000, 18(3):283-287. 10.1038/ 73723 10700142
    • (2000) Nat Biotechnol , vol.18 , Issue.3 , pp. 283-287
    • Skolnick, J.1    Fetrow, J.S.2    Kolinski, A.3
  • 5
    • 0032605828 scopus 로고    scopus 로고
    • Processing and analysis of CASP3 protein structure predictions
    • 10.1002/(SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W 10526349
    • Zemla A Venclovas C Moult J Fidelis K Processing and analysis of CASP3 protein structure predictions Proteins 1999, (Suppl 3):22-29. 10.1002/ (SICI)1097-0134(1999)37:3+<22::AID-PROT5>3.0.CO;2-W 10526349
    • (1999) Proteins , Issue.SUPPL. 3 , pp. 22-29
    • Zemla, A.1    Venclovas, C.2    Moult, J.3    Fidelis, K.4
  • 6
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • 10.1002/prot.20264 15476259
    • Zhang Y Skolnick J Scoring function for automated assessment of protein structure template quality Proteins 2004, 57:702-710. 10.1002/prot.20264 15476259
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 8
    • 28144448406 scopus 로고    scopus 로고
    • The victor/FRST function for model quality estimation
    • 10.1089/cmb.2005.12.1316 16379537
    • Tosatto SC The victor/FRST function for model quality estimation J Comput Biol 2005, 12(10):1316-1327. 10.1089/cmb.2005.12.1316 16379537
    • (2005) J Comput Biol , vol.12 , Issue.10 , pp. 1316-1327
    • Tosatto, S.C.1
  • 9
    • 24144437430 scopus 로고    scopus 로고
    • Improving sequence-based fold recognition by using 3D model quality assessment
    • 10.1093/bioinformatics/bti540 15955780
    • Pettitt CS McGuffin LJ Jones DT Improving sequence-based fold recognition by using 3D model quality assessment Bioinformatics 2005, 21(17):3509-3515. 10.1093/bioinformatics/bti540 15955780
    • (2005) Bioinformatics , vol.21 , Issue.17 , pp. 3509-3515
    • Pettitt, C.S.1    McGuffin, L.J.2    Jones, D.T.3
  • 10
    • 36749049687 scopus 로고    scopus 로고
    • Prediction of global and local model quality in CASP7 using Pcons and ProQ
    • 10.1002/prot.21774
    • Wallner B Elofsson A Prediction of global and local model quality in CASP7 using Pcons and ProQ Proteins 2007, 69(S8):184-193. 10.1002/ prot.21774
    • (2007) Proteins , vol.69 , Issue.S8 , pp. 184-193
    • Wallner, B.1    Elofsson, A.2
  • 11
    • 33645972948 scopus 로고    scopus 로고
    • Servers for protein structure prediction
    • 10.1016/j.sbi.2006.03.004 16546376
    • Fischer D Servers for protein structure prediction Current opinion in structural biology 2006, 16(2):178-182. 10.1016/j.sbi.2006.03.004 16546376
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.2 , pp. 178-182
    • Fischer, D.1
  • 12
    • 36749043625 scopus 로고    scopus 로고
    • Assessment of predictions in the model quality assessment category
    • 10.1002/prot.21669
    • Cozzetto D Kryshtafovych A Ceriani M Tramontano A Assessment of predictions in the model quality assessment category Proteins 2007, 69(S8):175-183. 10.1002/prot.21669
    • (2007) Proteins , vol.69 , Issue.S8 , pp. 175-183
    • Cozzetto, D.1    Kryshtafovych, A.2    Ceriani, M.3    Tramontano, A.4
  • 13
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: A local meta-threading-server for protein structure prediction
    • 1904280 17478507 10.1093/nar/gkm251
    • Wu ST Zhang Y LOMETS: A local meta-threading-server for protein structure prediction Nucl Acids Res 2007, 35:3375-3382. 1904280 17478507 10.1093/nar/gkm251
    • (2007) Nucl Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.T.1    Zhang, Y.2
  • 14
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • 419651 15126668 10.1073/pnas.0305695101
    • Zhang Y Skolnick J Automated structure prediction of weakly homologous proteins on a genomic scale Proceedings of the National Academy of Sciences of the United States of America 2004, 101:7594-7599. 419651 15126668 10.1073/pnas.0305695101
    • (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 15
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • 1878469 17488521 10.1186/1741-7007-5-17
    • Wu ST Skolnick J Zhang Y Ab initio modeling of small proteins by iterative TASSER simulations BMC Biology 2007, 5:17. 1878469 17488521 10.1186/1741-7007-5-17
    • (2007) BMC Biology , vol.5 , pp. 17
    • Wu, S.T.1    Skolnick, J.2    Zhang, Y.3
  • 16
    • 36749061828 scopus 로고    scopus 로고
    • Template-based modeling and free modeling by I-TASSER in CASP7
    • 10.1002/prot.21702
    • Zhang Y Template-based modeling and free modeling by I-TASSER in CASP7 Proteins 2007, 69(S8):108-117. 10.1002/prot.21702
    • (2007) Proteins , vol.69 , Issue.S8 , pp. 108-117
    • Zhang, Y.1
  • 17
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • 10.1093/bioinformatics/14.10.846 9927713
    • Karplus K Barrett C Hughey R Hidden Markov models for detecting remote protein homologies Bioinformatics 1998, 14:846-856. 10.1093/ bioinformatics/14.10.846 9927713
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 18
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • 146917 9254694 10.1093/nar/25.17.3389
    • Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic acids research 1997, 25(17):3389-3402. 146917 9254694 10.1093/nar/25.17.3389
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 19
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • 10.1016/0022-2836(70)90057-4 5420325
    • Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins Journal of molecular biology 1970, 48(3):443-453. 10.1016/0022-2836(70)90057-4 5420325
    • (1970) Journal of Molecular Biology , vol.48 , Issue.3 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 20
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • 10.1016/0022-2836(81)90087-5 7265238
    • Smith TF Waterman MS Identification of common molecular subsequences Journal of molecular biology 1981, 147(1):195-197. 10.1016/ 0022-2836(81)90087-5 7265238
    • (1981) Journal of Molecular Biology , vol.147 , Issue.1 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 21
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • 1303233 12885659
    • Zhang Y Kolinski A Skolnick J TOUCHSTONE II: A new approach to ab initio protein structure prediction Biophysical journal 2003, 85:1145-1164. 1303233 12885659
    • (2003) Biophysical Journal , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 22
    • 0036681386 scopus 로고    scopus 로고
    • Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
    • 10.1002/prot.10141 12112688
    • Zhang Y Kihara D Skolnick J Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding Proteins 2002, 48:192-201. 10.1002/prot.10141 12112688
    • (2002) Proteins , vol.48 , pp. 192-201
    • Zhang, Y.1    Kihara, D.2    Skolnick, J.3
  • 23
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • 10.1002/jcc.20011 15011258
    • Zhang Y Skolnick J SPICKER: A clustering approach to identify near-native protein folds Journal of computational chemistry 2004, 25(6):865-871. 10.1002/jcc.20011 15011258
    • (2004) Journal of Computational Chemistry , vol.25 , Issue.6 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 24
    • 84874647443 scopus 로고    scopus 로고
    • SPICKER package
    • SPICKER package http://zhang.bioinformatics.ku.edu/SPICKER
  • 25
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • 1084323 15849316 10.1093/nar/gki524
    • Zhang Y Skolnick J TM-align: A protein structure alignment algorithm based on the TM-score Nucleic acids research 2005, 33(7):2302-2309. 1084323 15849316 10.1093/nar/gki524
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 26
    • 0034308093 scopus 로고    scopus 로고
    • Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models
    • 10.1002/1097-0134(20001001)41:1<86::AID-PROT110>3.0.CO;2-Y 10944396
    • Feig M Rotkiewicz P Kolinski A Skolnick J Brooks CL 3rd Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models Proteins 2000, 41(1):86-97. 10.1002/ 1097-0134(20001001)41:1<86::AID-PROT110>3.0.CO;2-Y 10944396
    • (2000) Proteins , vol.41 , Issue.1 , pp. 86-97
    • Feig, M.1    Rotkiewicz, P.2    Kolinski, A.3    Skolnick, J.4    Brooks III, C.L.5
  • 27
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • 10.1110/ps.03154503 12930999
    • Canutescu AA Shelenkov AA Dunbrack RL Jr. A graph-theory algorithm for rapid protein side-chain prediction Protein Sci 2003, 12(9):2001-2014. 10.1110/ps.03154503 12930999
    • (2003) Protein Sci , vol.12 , Issue.9 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 28
    • 84874661029 scopus 로고    scopus 로고
    • I-TASSER queue
    • I-TASSER queue http://zhang.bioinformatics.ku.edu/I-TASSER/output.html
  • 29
    • 84874654859 scopus 로고    scopus 로고
    • About I-TASSER
    • About I-TASSER http://zhang.bioinformatics.ku.edu/I-TASSER/about.html
  • 31
    • 84874663506 scopus 로고    scopus 로고
    • Benchmark protein list
    • Benchmark protein list http://zhang.bioinformatics.ku.edu/I-TASSER/ decoys/proteins
  • 32
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W A solution for the best rotation to relate two sets of vectors Acta Cryst 1976, A32:922-923.
    • (1976) Acta Cryst , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 33
    • 0035888284 scopus 로고    scopus 로고
    • Universal similarity measure for comparing protein structures
    • 10.1002/1097-0282(20011015)59:5<305::AID-BIP1027>3.0.CO;2-6 11514933
    • Betancourt MR Skolnick J Universal similarity measure for comparing protein structures Biopolymers 2001, 59(5):305-309. 10.1002/ 1097-0282(20011015)59:5<305::AID-BIP1027>3.0.CO;2-6 11514933
    • (2001) Biopolymers , vol.59 , Issue.5 , pp. 305-309
    • Betancourt, M.R.1    Skolnick, J.2


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