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Volumn 11, Issue 10, 2015, Pages

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Author keywords

[No Author keywords available]

Indexed keywords

HEURISTIC METHODS; OPEN SYSTEMS; PROBABILITY; PROTEINS;

EID: 84946015803     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004343     Document Type: Article
Times cited : (108)

References (33)
  • 1
    • 80855132939 scopus 로고    scopus 로고
    • Assessment of template based protein structure predictions in CASP9
    • Mariani V, Kiefer F, Schmidt T, Haas J, Schwede T, (2011) Assessment of template based protein structure predictions in CASP9. Proteins 79 Suppl 1: 37–58. 22002823
    • (2011) Proteins , vol.79 , pp. 37-58
    • Mariani, V.1    Kiefer, F.2    Schmidt, T.3    Haas, J.4    Schwede, T.5
  • 2
    • 80855133462 scopus 로고    scopus 로고
    • CASP9 assessment of free modeling target predictions
    • Kinch L, Yong Shi S, Cong Q, Cheng H, Liao Y, et al. (2011) CASP9 assessment of free modeling target predictions. Proteins 79 Suppl 10: 59–73. doi: 10.1002/prot.23181 21997521
    • (2011) Proteins , vol.79 , pp. 59-73
    • Kinch, L.1    Yong Shi, S.2    Cong, Q.3    Cheng, H.4    Liao, Y.5
  • 3
    • 84892959896 scopus 로고    scopus 로고
    • Assessment of template-based protein structure predictions in CASP10
    • Huang Yea, (2013) Assessment of template-based protein structure predictions in CASP10. Proteins 2: 43–56.
    • (2013) Proteins , vol.2 , pp. 43-56
    • Huang, Y.1
  • 4
    • 84901271941 scopus 로고    scopus 로고
    • A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction
    • Yan R, Xu D, Yang J, Walker S, Zhang Y, (2013) A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Scientific reports 3: 2619. doi: 10.1038/srep02619 24018415
    • (2013) Scientific reports , vol.3 , pp. 2619
    • Yan, R.1    Xu, D.2    Yang, J.3    Walker, S.4    Zhang, Y.5
  • 5
    • 84892968997 scopus 로고    scopus 로고
    • CASP10 results compared to those of previous CASP experiments
    • Kryshtafovych Aea, (2014) CASP10 results compared to those of previous CASP experiments. Proteins 82: 164–174. doi: 10.1002/prot.24448
    • (2014) Proteins , vol.82 , pp. 164-174
    • Kryshtafovych, A.1
  • 6
    • 79958058080 scopus 로고    scopus 로고
    • Protein sequence comparison and fold recognition: progress and good-practice benchmarking
    • Söding J, Remmert M, (2011) Protein sequence comparison and fold recognition: progress and good-practice benchmarking. Current opinion in structural biology 21: 404–11. doi: 10.1016/j.sbi.2011.03.005 21458982
    • (2011) Current opinion in structural biology , vol.21 , pp. 404-411
    • Söding, J.1    Remmert, M.2
  • 7
    • 17744387920 scopus 로고    scopus 로고
    • All are not equal: A benchmark of different homology modeling programs
    • Wallner B, Elofsson A, (2005) All are not equal: A benchmark of different homology modeling programs. Protein Science 15: 1315–1327. doi: 10.1110/ps.041253405
    • (2005) Protein Science , vol.15 , pp. 1315-1327
    • Wallner, B.1    Elofsson, A.2
  • 8
    • 34548136236 scopus 로고    scopus 로고
    • An evaluation of automated homology modelling methods at low target template sequence similarity
    • Dalton JaR, Jackson RM, (2007) An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 23: 1901–8. doi: 10.1093/bioinformatics/btm262 17510171
    • (2007) Bioinformatics , vol.23 , pp. 1901-1908
    • Dalton, J.R.1    Jackson, R.M.2
  • 9
    • 0026754015 scopus 로고    scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt M, (1996) Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226: 507–533. doi: 10.1016/0022-2836(92)90964-L
    • (1996) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 10
    • 0042622380 scopus 로고    scopus 로고
    • Swiss-model: an automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, Peitsch M, (2003) Swiss-model: an automated protein homology-modeling server. Nuc Acid Res 31: 3381–85. doi: 10.1093/nar/gkg520
    • (2003) Nuc Acid Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.4
  • 11
    • 10744220076 scopus 로고    scopus 로고
    • Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
    • Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, et al. (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53 Suppl 6: 430–435. doi: 10.1002/prot.10550 14579332
    • (2003) Proteins , vol.53 , pp. 430-435
    • Petrey, D.1    Xiang, Z.2    Tang, C.L.3    Xie, L.4    Gimpelev, M.5
  • 12
    • 0027136282 scopus 로고
    • Comparative Protein Modelling by Satisfaction of Spatial Restraints
    • Sali A, Blundell T, (1993) Comparative Protein Modelling by Satisfaction of Spatial Restraints. J Mol Biol 234: 779–815. doi: 10.1006/jmbi.1993.1626 8254673
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.2
  • 13
    • 69849109596 scopus 로고    scopus 로고
    • All-atom chain-building by optimizing MODELLER energy function using conformational space annealing
    • Joo K, Lee J, Seo JH, Lee K, Kim BG, et al. (2009) All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins 75: 1010–23. doi: 10.1002/prot.22312 19089941
    • (2009) Proteins , vol.75 , pp. 1010-1023
    • Joo, K.1    Lee, J.2    Seo, J.H.3    Lee, K.4    Kim, B.G.5
  • 15
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Söding J, (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature methods 9: 173–5. doi: 10.1038/nmeth.1818
    • (2012) Nature methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Söding, J.4
  • 18
    • 0024974791 scopus 로고
    • Weights for data related by a tree
    • Altschul S, Carroll R, DJ L, (1989) Weights for data related by a tree. J Mol Biol 207: 647–653. doi: 10.1016/0022-2836(89)90234-9 2760928
    • (1989) J Mol Biol , vol.207 , pp. 647-653
    • Altschul, S.1    Carroll, R.2    Dj, L.3
  • 19
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal R, Michener C, (1958) A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin 38: 1409–38.
    • (1958) University of Kansas Science Bulletin , vol.38 , pp. 1409-1438
    • Sokal, R.1    Michener, C.2
  • 20
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J, (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic acids research 33: 2302–9. doi: 10.1093/nar/gki524 15849316
    • (2005) Nucleic acids research , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 22
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • Hildebrand A, Remmert M, Biegert A, Söding J, (2009) Fast and accurate automatic structure prediction with HHpred. Proteins 77 Suppl 9: 128–32. doi: 10.1002/prot.22499 19626712
    • (2009) Proteins , vol.77 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Söding, J.4
  • 23
    • 80855147852 scopus 로고    scopus 로고
    • RaptorX: exploiting structure information for protein alignment by statistical inference
    • Peng J, Xu J, (2011) RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins 79 Suppl 1: 161–71. doi: 10.1002/prot.23175 21987485
    • (2011) Proteins , vol.79 , pp. 161-171
    • Peng, J.1    Xu, J.2
  • 24
    • 42149153292 scopus 로고    scopus 로고
    • A multi-template combination algorithm for protein comparative modeling
    • Cheng J, (2008) A multi-template combination algorithm for protein comparative modeling. BMC structural biology 8: 18. doi: 10.1186/1472-6807-8-18 18366648
    • (2008) BMC structural biology , vol.8 , pp. 18
    • Cheng, J.1
  • 25
    • 35748965848 scopus 로고    scopus 로고
    • Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
    • Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A, (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23: 2558–65. doi: 10.1093/bioinformatics/btm377 17823132
    • (2007) Bioinformatics , vol.23 , pp. 2558-2565
    • Fernandez-Fuentes, N.1    Rai, B.K.2    Madrid-Aliste, C.J.3    Fajardo, J.E.4    Fiser, A.5
  • 26
    • 77951941264 scopus 로고    scopus 로고
    • MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8
    • Wang Z, Eickholt J, Cheng J, (2010) MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 26: 882–8. doi: 10.1093/bioinformatics/btq058 20150411
    • (2010) Bioinformatics , vol.26 , pp. 882-888
    • Wang, Z.1    Eickholt, J.2    Cheng, J.3
  • 27
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang Y, (2008) I-TASSER server for protein 3D structure prediction. BMC bioinformatics 9: 40. doi: 10.1186/1471-2105-9-40 18215316
    • (2008) BMC bioinformatics , vol.9 , pp. 40
    • Zhang, Y.1
  • 28
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A Clustering Approach to Identify Near-Native
    • Zhang Y, Skolnick J, (2004) SPICKER: A Clustering Approach to Identify Near-Native. J Comput Chem 25: 865–871. doi: 10.1002/jcc.20011 15011258
    • (2004) J Comput Chem , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 29
    • 36749059956 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions in the high accuracy template-based modeling category
    • Read RJ, Chavali G, (2007) Assessment of CASP7 predictions in the high accuracy template-based modeling category. Proteins 69: 27–37. doi: 10.1002/prot.21662 17894351
    • (2007) Proteins , vol.69 , pp. 27-37
    • Read, R.J.1    Chavali, G.2
  • 30
    • 44349091007 scopus 로고    scopus 로고
    • Using multiple templates to improve quality of homology models in automated homology modeling
    • Larsson P, Wallner B, Lindahl E, Elofsson A, (2008) Using multiple templates to improve quality of homology models in automated homology modeling. Protein Science: 990–1002. doi: 10.1110/ps.073344908 18441233
    • (2008) Protein Science , pp. 990-1002
    • Larsson, P.1    Wallner, B.2    Lindahl, E.3    Elofsson, A.4
  • 31
    • 84946033771 scopus 로고    scopus 로고
    • Casp9 abstract book: the embo conference (2010). URL http://predictioncenter.org/casp9/doc/Abstracts.pdf.
  • 32
    • 84946019860 scopus 로고    scopus 로고
    • Casp10 abstract book: the embo conference (2012). URL http://predictioncenter.org/casp10/doc/CASP10_Abstracts.pdf.
  • 33
    • 84856497340 scopus 로고    scopus 로고
    • Putting the pieces together: Integrative modeling platform software for strucutre determination of macromolecular assemblies
    • Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, et al. (2012) Putting the pieces together: Integrative modeling platform software for strucutre determination of macromolecular assemblies. PLoS Biol 10. doi: 10.1371/journal.pbio.1001244 22272186
    • (2012) PLoS Biol , vol.10
    • Russel, D.1    Lasker, K.2    Webb, B.3    Velazquez-Muriel, J.4    Tjioe, E.5


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