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Volumn 91, Issue 11, 2006, Pages 4180-4190

TASSER-lite: An automated tool for protein comparative modeling

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; INTERMETHOD COMPARISON; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; QUALITY CONTROL;

EID: 33845365051     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.084293     Document Type: Article
Times cited : (44)

References (43)
  • 1
    • 0033964710 scopus 로고    scopus 로고
    • From genes to protein structure and function: Novel applications of computational approaches in the genomic era
    • Skolnick, J., and J. S. Fetrow. 2000. From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol. 18:34-39.
    • (2000) Trends Biotechnol. , vol.18 , pp. 34-39
    • Skolnick, J.1    Fetrow, J.S.2
  • 2
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker, D., and A. Sali. 2001. Protein structure prediction and structural genomics. Science. 294:93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 3
    • 0035150828 scopus 로고    scopus 로고
    • Progress in protein structure prediction
    • Murzin, A. G. 2001. Progress in protein structure prediction. Nat. Struct. Biol. 8:110-112.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 110-112
    • Murzin, A.G.1
  • 4
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex, N., and M. C. Peitsch. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18:2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 5
    • 0030908273 scopus 로고    scopus 로고
    • Advances in comparative protein-structure modelling
    • Sanchez, R., and A. Sali. 1997. Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7:206-214.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 206-214
    • Sanchez, R.1    Sali, A.2
  • 6
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie, J. U., R. Luthy, and D. Eisenberg. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 7
    • 0034628922 scopus 로고    scopus 로고
    • Combination of threading potentials and sequence profiles improves fold recognition
    • Panchenko, A. R., A. Marchler-Bauer, and S. H. Bryant. 2000. Combination of threading potentials and sequence profiles improves fold recognition. J. Mol. Biol. 296:1319-1331.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1319-1331
    • Panchenko, A.R.1    Marchler-Bauer, A.2    Bryant, S.H.3
  • 8
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
    • Skolnick, J., and D. Kihara. 2001. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins. 42:319-331.
    • (2001) Proteins , vol.42 , pp. 319-331
    • Skolnick, J.1    Kihara, D.2
  • 10
    • 0035830958 scopus 로고    scopus 로고
    • Prospects for ab initio protein structural genomics
    • Simons, K. T., C. Strauss, and D. Baker. 2001. Prospects for ab initio protein structural genomics. J. Mol. Biol. 306:1191-1199.
    • (2001) J. Mol. Biol. , vol.306 , pp. 1191-1199
    • Simons, K.T.1    Strauss, C.2    Baker, D.3
  • 11
    • 0031855094 scopus 로고    scopus 로고
    • Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model
    • Kolinski, A., and J. Skolnick. 1998. Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32:475-494.
    • (1998) Proteins , vol.32 , pp. 475-494
    • Kolinski, A.1    Skolnick, J.2
  • 12
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L., and C. Sander. 1996. Mapping the protein universe. Science. 273:595-603.
    • (1996) Science , vol.273 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 13
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C., and A. M. Lesk. 1986. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 15
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang, Y., and J. Skolnick. 2005. The protein structure prediction problem could be solved using the current PDB library. Proc. Natl. Acad. Sci. USA. 102:1029-1034.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2
  • 16
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell, T. L., B. L. Sibanda, M. J. Sternberg, and J. M. Thornton. 1987. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326:347-352.
    • (1987) Nature , vol.326 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.3    Thornton, J.M.4
  • 17
    • 0027220648 scopus 로고
    • An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure
    • Srinivasan, N., and T. L. Blundell. 1993. An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng. 6:501-512.
    • (1993) Protein Eng. , vol.6 , pp. 501-512
    • Srinivasan, N.1    Blundell, T.L.2
  • 18
    • 0024527223 scopus 로고
    • Modelling the polypeptide backbone with 'spare parts' from known protein structures
    • Claessens, M., E. Van Cutsem, I. Lasters, and S. Wodak. 1989. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng. 2:335-345.
    • (1989) Protein Eng. , vol.2 , pp. 335-345
    • Claessens, M.1    Van Cutsem, E.2    Lasters, I.3    Wodak, S.4
  • 19
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones, T. A., and S. Thirup. 1986. Using known substructures in protein model building and crystallography. EMBO J. 5:819-822.
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 20
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt, M. 1992. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226:507-533.
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 21
    • 0030322828 scopus 로고    scopus 로고
    • Homology modeling by distance geometry
    • Aszodi, A., and W. R. Taylor. 1996. Homology modeling by distance geometry. Fold. Des. 1:325-334.
    • (1996) Fold. Des. , vol.1 , pp. 325-334
    • Aszodi, A.1    Taylor, W.R.2
  • 22
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A., and T. L. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 23
    • 0027510701 scopus 로고
    • An automated method for modeling proteins on known templates using distance geometry
    • Srinivasan, S., C. J. March, and S. Sudarsanam. 1993. An automated method for modeling proteins on known templates using distance geometry. Protein Sci. 2:277-289.
    • (1993) Protein Sci. , vol.2 , pp. 277-289
    • Srinivasan, S.1    March, C.J.2    Sudarsanam, S.3
  • 25
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser, A., R. K. Do, and A. Sali. 2000. Modeling of loops in protein structures. Protein Sci. 9:1753-1773.
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 26
    • 0345871261 scopus 로고    scopus 로고
    • Exploiting evolutionary relationships for predicting protein structures
    • Tramontano, A., and V. Morea. 2003. Exploiting evolutionary relationships for predicting protein structures. Biotechnol. Bioeng. 84:756-762.
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 756-762
    • Tramontano, A.1    Morea, V.2
  • 27
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang, Y., and J. Skolnick. 2004. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc. Natl. Acad. Sci. USA. 101:7594-7599.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 28
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm
    • Skolnick, J., D. Kihara, and Y. Zhang. 2004. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins. 56:502-518.
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 29
    • 16644386061 scopus 로고    scopus 로고
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
    • Zhang, Y., and J. Skolnick. 2004. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys. J. 87:2647-2655.
    • (2004) Biophys. J. , vol.87 , pp. 2647-2655
    • Zhang, Y.1    Skolnick, J.2
  • 30
    • 30344488120 scopus 로고    scopus 로고
    • TASSER: An automated method for the prediction of protein tertiary structures in CASP6
    • Zhang, Y., A. K. Arakaki, and J. Skolnick. 2005. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 61(Suppl. 7):91-98.
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 91-98
    • Zhang, Y.1    Arakaki, A.K.2    Skolnick, J.3
  • 33
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang, Y., A. Kolinski, and J. Skolnick. 2003. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys. J. 85:1145-1164.
    • (2003) Biophys. J. , vol.85 , pp. 1145-1164
    • Zhang, Y.1    Kolinski, A.2    Skolnick, J.3
  • 36
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: A clustering approach to identify near-native protein folds
    • Zhang, Y., and J. Skolnick. 2004. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 25:865-871.
    • (2004) J. Comput. Chem. , vol.25 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 37
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 38
    • 0036681386 scopus 로고    scopus 로고
    • Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding
    • Zhang, Y., D. Kihara, and J. Skolnick. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48:192-201.
    • (2002) Proteins , vol.48 , pp. 192-201
    • Zhang, Y.1    Kihara, D.2    Skolnick, J.3
  • 39
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang, Y., and J. Skolnick. 2004. Scoring function for automated assessment of protein structure template quality. Proteins. 57:702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 40
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A. G., S. E. Brenner, T. Hubbard, and C. Chothia. 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 41
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabash, W. 1978. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A32:922-923.
    • (1978) Acta Crystallogr. , vol.A32 , pp. 922-923
    • Kabash, W.1
  • 42
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: An automated measure for the assessment of protein structure prediction quality
    • Siew, N., A. Elofsson, L. Rychlewski, and D. Fischer. 2000. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics. 16:776-785.
    • (2000) Bioinformatics , vol.16 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 43
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Zhang, Y., and J. Skolnick. 2005. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33:2302-2309.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


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