메뉴 건너뛰기




Volumn 17, Issue 2, 2010, Pages 153-168

BCL::Contact-low confidence fold recognition hits boost protein contact prediction and de novo structure determination

Author keywords

CASP; Computational structural biology; Contact prediction; Structure prediction.

Indexed keywords

CASP7 PROTEIN, HUMAN; CASPASE 7;

EID: 77249140522     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2009.0030     Document Type: Article
Times cited : (5)

References (65)
  • 1
    • 0024084164 scopus 로고
    • Coordinated amino acid changes in homologous protein families
    • Altschuh, D., Vernet, T., Berti, P., et al. 1988. Coordinated amino acid changes in homologous protein families. Protein Eng. 2, 193-199.
    • (1988) Protein Eng , vol.2 , pp. 193-199
    • Altschuh, D.1    Vernet, T.2    Berti, P.3
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S.F., Madden, T.L., Schäffer, A.A., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3
  • 3
    • 0029097099 scopus 로고
    • Global fold determination from a small number of distance restraints
    • Aszodi, A., Gradwell, M.J., and Taylor, W.R. 1995. Global fold determination from a small number of distance restraints. J. Mol. Biol. 251, 308-326.
    • (1995) J. Mol. Biol , vol.251 , pp. 308-326
    • Aszodi, A.1    Gradwell, M.J.2    Taylor, W.R.3
  • 4
    • 0034604105 scopus 로고    scopus 로고
    • A surprising simplicity to protein folding
    • Baker, D. 2000. A surprising simplicity to protein folding. Nature 405, 39-42.
    • (2000) Nature , vol.405 , pp. 39-42
    • Baker, D.1
  • 5
    • 0036073603 scopus 로고    scopus 로고
    • Contact order and abinitio protein structure prediction
    • Bonneau, R., Ruczinski, I., Tsai, J., et al. 2002a. Contact order and abinitio protein structure prediction. Protein Sci. 11, 1937-1944.
    • (2002) Protein Sci , vol.11 , pp. 1937-1944
    • Bonneau, R.1    Ruczinski, I.2    Tsai, J.3
  • 6
    • 0036968925 scopus 로고    scopus 로고
    • De novo prediction of three-dimensional structures for major protein families
    • Bonneau, R., Strauss, C.E.M., Rohl, C., et al. 2002b. De novo prediction of three-dimensional structures for major protein families. J. Mol. Biol. 322, 65-78.
    • (2002) J. Mol. Biol , vol.322 , pp. 65-78
    • Bonneau, R.1    Strauss, C.E.M.2    Rohl, C.3
  • 7
    • 0035103763 scopus 로고    scopus 로고
    • LiveBench-1: Continuous benchmarking of protein structure prediction servers
    • Bujnicki, J.M., Elofsson, A., Fischer, D., et al. 2001. LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci. 10, 352-361.
    • (2001) Protein Sci , vol.10 , pp. 352-361
    • Bujnicki, J.M.1    Elofsson, A.2    Fischer, D.3
  • 8
    • 33745616114 scopus 로고    scopus 로고
    • A machine learning information retrieval approach to protein fold recognition
    • Cheng, J., and Baldi, P. 2006. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 22, 1456-1463.
    • (2006) Bioinformatics , vol.22 , pp. 1456-1463
    • Cheng, J.1    Baldi, P.2
  • 9
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • Cheng, J., and Baldi, P. 2007. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinform. 8, 113.
    • (2007) BMC Bioinform , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 10
    • 33750210515 scopus 로고    scopus 로고
    • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    • Chivian, D., and Baker, D. 2006. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 34, e112.
    • (2006) Nucleic Acids Res , vol.34
    • Chivian, D.1    Baker, D.2
  • 11
    • 30344443955 scopus 로고    scopus 로고
    • Prediction of CASP-6 structures using automated Robetta protocols
    • Chivian, D., Kim, D.E., Malmstrom, L., et al. 2005. Prediction of CASP-6 structures using automated Robetta protocols. Proteins 61, 157-166.
    • (2005) Proteins , vol.61 , pp. 157-166
    • Chivian, D.1    Kim, D.E.2    Malmstrom, L.3
  • 12
    • 33748449489 scopus 로고    scopus 로고
    • STRUCTFAST: Protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring
    • Debe, D.A., Danzer, J.F., Goddard, W.A., et al. 2006. STRUCTFAST: protein sequence remote homology detection and alignment using novel dynamic programming and profile-profile scoring. Proteins 64, 960-967.
    • (2006) Proteins , vol.64 , pp. 960-967
    • Debe, D.A.1    Danzer, J.F.2    Goddard, W.A.3
  • 13
    • 0033047710 scopus 로고    scopus 로고
    • A neural network based predictor of residue contacts in proteins
    • Fariselli, P., and Casadio, R. 1999. A neural network based predictor of residue contacts in proteins. Protein Eng. 12, 15-21.
    • (1999) Protein Eng , vol.12 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 14
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • Fariselli, P., Olmea, O., Valencia, A., et al. 2001a. Prediction of contact maps with neural networks and correlated mutations. Protein Eng. 14, 835-843.
    • (2001) Protein Eng , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3
  • 15
    • 0035700864 scopus 로고    scopus 로고
    • Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations
    • Fariselli, P., Olmea, O., Valencia, A., et al. 2001b. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. Proteins Suppl 5, 157-162.
    • (2001) Proteins Suppl , vol.5 , pp. 157-162
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3
  • 16
    • 0242299173 scopus 로고    scopus 로고
    • 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3
    • Fischer, D. 2003. 3DS3 and 3DS5 3D-SHOTGUN meta-predictors in CAFASP3. Proteins 53, 517-523.
    • (2003) Proteins , vol.53 , pp. 517-523
    • Fischer, D.1
  • 17
    • 0242299155 scopus 로고    scopus 로고
    • CAFASP3: The third critical assessment of fully automated structure prediction methods
    • Fischer, D., Rychlewski, L., Dunbrack, R.L., Jr., et al. 2003. CAFASP3: the third critical assessment of fully automated structure prediction methods. Proteins 53, 503-516.
    • (2003) Proteins , vol.53 , pp. 503-516
    • Fischer, D.1    Rychlewski, L.2    Dunbrack, Jr.R.L.3
  • 18
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski, K., Elofsson, A., Fischer, D., et al. 2003a. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19, 1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3
  • 19
    • 0042121000 scopus 로고    scopus 로고
    • ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure
    • Ginalski, K., Pas, J., Wyrwicz, L.S., et al. 2003b. ORFeus: Detection of distant homology using sequence profiles and predicted secondary structure. Nucleic Acids Res. 31, 3804-3807.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3804-3807
    • Ginalski, K.1    Pas, J.2    Wyrwicz, L.S.3
  • 20
    • 0041620404 scopus 로고    scopus 로고
    • Detection of reliable and unexpected protein fold predictions using 3D-Jury
    • Ginalski, K., and Rychlewski, L. 2003. Detection of reliable and unexpected protein fold predictions using 3D-Jury. Nucleic Acids Res. 31, 3291-3292.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3291-3292
    • Ginalski, K.1    Rychlewski, L.2
  • 21
    • 0028295169 scopus 로고
    • Correlated mutations and residue contacts in proteins
    • Gobel, U., Sander, C., Schneider, R., et al. 1994. Correlated mutations and residue contacts in proteins. Proteins 18, 309-317.
    • (1994) Proteins , vol.18 , pp. 309-317
    • Gobel, U.1    Sander, C.2    Schneider, R.3
  • 22
    • 30344453347 scopus 로고    scopus 로고
    • CASP6 assessment of contact prediction
    • Grana, O., Baker, D., MacCallum, R.M., et al. 2005. CASP6 assessment of contact prediction. Proteins 61, 214-224.
    • (2005) Proteins , vol.61 , pp. 214-224
    • Grana, O.1    Baker, D.2    Mac Callum, R.M.3
  • 23
    • 33646766064 scopus 로고    scopus 로고
    • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families
    • Halperin, I., Wolfson, H., and Nussinov, R. 2006. Correlated mutations: adVances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins 63, 832-845.
    • (2006) Proteins , vol.63 , pp. 832-845
    • Halperin, I.1    Wolfson, H.2    Nussinov, R.3
  • 24
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using patterns of correlation
    • Hamilton, N., Burrage, K., Ragan, M.A., et al. 2004. Protein contact prediction using patterns of correlation. Proteins 56, 679-684.
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.A.3
  • 25
    • 0033516514 scopus 로고    scopus 로고
    • Abinitio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
    • Huang, E.S., Samudrala, R., and Ponder, J.W. 1999. Abinitio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J. Mol. Biol. 290, 267-281.
    • (1999) J. Mol. Biol , vol.290 , pp. 267-281
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 26
    • 36749082814 scopus 로고    scopus 로고
    • Assessment of intramolecular contact predictions for CASP7
    • Izarzugaza, J.M., Grana, O., Tress, M.L., et al. 2007. Assessment of intramolecular contact predictions for CASP7. Proteins 69, 152-158.
    • (2007) Proteins , vol.69 , pp. 152-158
    • Izarzugaza, J.M.1    Grana, O.2    Tress, M.L.3
  • 27
    • 23144463912 scopus 로고    scopus 로고
    • FFAS03: A server for profile-profile sequence alignments
    • Jaroszewski, L., Rychlewski, L., Li, Z., et al. 2005. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33, W284-W288.
    • (2005) Nucleic Acids Res , vol.33
    • Jaroszewski, L.1    Rychlewski, L.2    Li, Z.3
  • 28
    • 0033537993 scopus 로고    scopus 로고
    • Gen threader: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones, D.T. 1999. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815.
    • (1999) J. Mol. Biol , vol.287 , pp. 797-815
    • Jones, D.T.1
  • 29
    • 0034855972 scopus 로고    scopus 로고
    • Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
    • Karplus, K., and Hu, B. 2001. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 17, 713-720.
    • (2001) Bioinformatics , vol.17 , pp. 713-720
    • Karplus, K.1    Hu, B.2
  • 30
    • 30344452280 scopus 로고    scopus 로고
    • SAM-T04: What is new in protein-structure prediction for CASP6
    • Karplus, K., Katzman, S., Shackleford, G., et al. 2005. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 61, 135-142.
    • (2005) Proteins , vol.61 , pp. 135-142
    • Karplus, K.1    Katzman, S.2    Shackleford, G.3
  • 31
    • 33751219893 scopus 로고    scopus 로고
    • Predicting residue contacts using pragmatic correlated mutations method: Reducing the false positives
    • Kundrotas, P.J., and Alexov, E.G. 2006. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC Bioinform. 7, 503.
    • (2006) BMC Bioinform , vol.7 , pp. 503
    • Kundrotas, P.J.1    Alexov, E.G.2
  • 32
    • 50349097782 scopus 로고    scopus 로고
    • Benchmarking of TASSER 2.0: An improved protein structure prediction algorithm with more accurate predicted contact restraints
    • Lee, S.Y., and Skolnick, J. 2008. Benchmarking of TASSER 2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys. J. 95, 1956-1964.
    • (2008) Biophys. J , vol.95 , pp. 1956-1964
    • Lee, S.Y.1    Skolnick, J.2
  • 33
    • 4143110064 scopus 로고    scopus 로고
    • Application of sparse NMR restraints to large-scale protein structure prediction
    • Li, W., Zhang, Y., and Skolnick, J. 2004. Application of sparse NMR restraints to large-scale protein structure prediction. Biophys. J. 87, 1241-1248.
    • (2004) Biophys. J , vol.87 , pp. 1241-1248
    • Li, W.1    Zhang, Y.2    Skolnick, J.3
  • 34
    • 0031406438 scopus 로고    scopus 로고
    • Protein distance constraints predicted by neural networks and probability density functions
    • Lund, O., Frimand, K., Gorodkin, J., et al. 1997. Protein distance constraints predicted by neural networks and probability density functions. Protein Eng. 10, 1241-1248.
    • (1997) Protein Eng , vol.10 , pp. 1241-1248
    • Lund, O.1    Frimand, K.2    Gorodkin, J.3
  • 35
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: A neural-network -based consensus predictor that improves fold recognition
    • Lundstroem, J., Rychlewski, L., Bujnicki, J., et al. 2001. Pcons: a neural-network -based consensus predictor that improves fold recognition. Protein Sci. 10, 2354-2362.
    • (2001) Protein Sci , vol.10 , pp. 2354-2362
    • Lundstroem, J.1    Rychlewski, L.2    Bujnicki, J.3
  • 36
    • 0038634975 scopus 로고    scopus 로고
    • Improvement of the Gen THREADER method for genomic fold recognition
    • McGuffin, L.J., and Jones, D.T. 2003. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19, 874-881.
    • (2003) Bioinformatics , vol.19 , pp. 874-881
    • Mc Guffin, L.J.1    Jones, D.T.2
  • 37
    • 0142027795 scopus 로고    scopus 로고
    • Coupled prediction of protein secondary and tertiary structure
    • Meiler, J., and Baker, D. 2003. Coupled prediction of protein secondary and tertiary structure. Proc. Natl. Acad. Sci. USA 100, 12105-12110.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 12105-12110
    • Meiler, J.1    Baker, D.2
  • 38
    • 0035789525 scopus 로고    scopus 로고
    • Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks
    • Meiler, J., Mü ller, M., Zeidler, A., et al. 2001. Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks. J. Mol. Model. 7, 360-369.
    • (2001) J. Mol. Model. , vol.7 , pp. 360-369
    • Meiler, J.1    Mü Ller, M.2    Zeidler, A.3
  • 39
    • 0033550256 scopus 로고    scopus 로고
    • Effective use of sequence correlation and conservation in fold recognition
    • Olmea, O., Rost, B., and Valencia, A. 1999. Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol. 293, 1221-1239.
    • (1999) J. Mol. Biol , vol.293 , pp. 1221-1239
    • Olmea, O.1    Rost, B.2    Valencia, A.3
  • 40
    • 0030627941 scopus 로고    scopus 로고
    • Improving contact predictions by the combination of correlated mutations and other sources of sequence information
    • Olmea, O., and Valencia, A. 1997. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des. 2, S25-S32.
    • (1997) Fold des , vol.2
    • Olmea, O.1    Valencia, A.2
  • 41
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz, A.R., Strauss, C.E.M., and Olmea, O. 2002. MAMMOTH (Matching molecular models obtained from theory): an automated method for model comparison. Protein Sci. 11, 2606-2611.
    • (2002) Protein Sci , vol.11 , pp. 2606-2611
    • Ortiz, A.R.1    Strauss, C.E.M.2    Olmea, O.3
  • 42
    • 0034724558 scopus 로고    scopus 로고
    • Evolutionary conservation in protein folding kinetics
    • Plaxco, K.W., Larson, S., Ruczinski, I., et al. 2000. Evolutionary conservation in protein folding kinetics. J. Mol. Biol. 298, 303-312.
    • (2000) J. Mol. Biol , vol.298 , pp. 303-312
    • Plaxco, K.W.1    Larson, S.2    Ruczinski, I.3
  • 43
    • 0041719954 scopus 로고    scopus 로고
    • Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
    • Pollastri, G., and Baldi, P. 2002. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 18, S62-S70.
    • (2002) Bioinformatics , vol.18
    • Pollastri, G.1    Baldi, P.2
  • 44
    • 0035237804 scopus 로고    scopus 로고
    • Improved prediction of the number of residue contacts in proteins by recurrent neural networks
    • Pollastri, G., Baldi, P., Fariselli, P., et al. 2001. Improved prediction of the number of residue contacts in proteins by recurrent neural networks. Bioinformatics 17, S234-S242.
    • (2001) Bioinformatics , vol.17
    • Pollastri, G.1    Baldi, P.2    Fariselli, P.3
  • 45
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock, D.D., Taylor, W.R., and Goldman, N. 1999. Coevolving protein residues: maximum likelihood identification and relationship to structure. J. Mol. Biol. 287, 187-198.
    • (1999) J. Mol. Biol , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 46
    • 21444454088 scopus 로고    scopus 로고
    • PROFcon: Novel prediction of long-range contacts
    • Punta, M., and Rost, B. 2005a. PROFcon: novel prediction of long-range contacts. Bioinformatics 21, 2960-2968.
    • (2005) Bioinformatics , vol.21 , pp. 2960-2968
    • Punta, M.1    Rost, B.2
  • 47
    • 17144369578 scopus 로고    scopus 로고
    • Protein folding rates estimated from contact predictions
    • Punta, M., and Rost, B. 2005b. Protein folding rates estimated from contact predictions. J. Mol. Biol. 348, 507-512.
    • (2005) J. Mol. Biol , vol.348 , pp. 507-512
    • Punta, M.1    Rost, B.2
  • 48
    • 0031909873 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds- Assessment of prediction success and associated alignment accuracy using empirical substitution matrices
    • Russell, R.B., Saqi, M.A., Bates, P.A., et al. 1998. Recognition of analogous and homologous protein folds- assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Protein Eng. 11, 1-9.
    • (1998) Protein Eng , vol.11 , pp. 1-9
    • Russell, R.B.1    Saqi, M.A.2    Bates, P.A.3
  • 49
    • 11144241105 scopus 로고    scopus 로고
    • LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction
    • Rychlewski, L., and Fischer, D. 2005. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci. 14, 240-245.
    • (2005) Protein Sci , vol.14 , pp. 240-245
    • Rychlewski, L.1    Fischer, D.2
  • 50
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A., and Blundell, T.L. 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
  • 51
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • Shackelford, G., and Karplus, K. 2007. Contact prediction using mutual information and neural nets. Proteins 69, 159-164.
    • (2007) Proteins , vol.69 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 52
    • 0042721397 scopus 로고    scopus 로고
    • Predicting interresidue contacts using templates and pathways
    • Shao, Y., and Bystroff, C. 2003. Predicting interresidue contacts using templates and pathways. Proteins 53, 497-502.
    • (2003) Proteins , vol.53 , pp. 497-502
    • Shao, Y.1    Bystroff, C.2
  • 53
    • 0035967880 scopus 로고    scopus 로고
    • FUGUE: Sequence-structure homology recognition using environmentspecific substitution tables and structure-dependent gap penalties
    • Shi, J., Blundell, T.L., and Mizuguchi, K. 2001. FUGUE: sequence-structure homology recognition using environmentspecific substitution tables and structure-dependent gap penalties. J. Mol. Biol. 310, 243-257.
    • (2001) J. Mol. Biol , vol.310 , pp. 243-257
    • Shi, J.1    Blundell, T.L.2    Mizuguchi, K.3
  • 54
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    • Shindyalov, I.N., Kolchanov, N.A., and Sander, C. 1994. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7, 349-358.
    • (1994) Protein Eng , vol.7 , pp. 349-358
    • Shindyalov, I.N.1    Kolchanov, N.A.2    Sander, C.3
  • 55
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons, K.T., Kooperberg, C., Huang, E., et al. 1997. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268, 209-225.
    • (1997) J. Mol. Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3
  • 56
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: Prospector-a new approach to threading
    • Skolnick, J., and Kihara, D. 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
  • 57
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3 threading algorithm
    • Skolnick, J., Kihara, D., and Zhang, Y. 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
  • 58
    • 30344463291 scopus 로고    scopus 로고
    • Protein structure prediction using a variety of profile libraries and 3D verification
    • Tomii, K., Hirokawa, T., and Motono, C. 2005. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 61, 114-121.
    • (2005) Proteins , vol.61 , pp. 114-121
    • Tomii, K.1    Hirokawa, T.2    Motono, C.3
  • 59
    • 3242889054 scopus 로고    scopus 로고
    • Wurst: A protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
    • Torda, A.E., Procter, J.B., and Huber, T. 2004. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res. 32, W532-535.
    • (2004) Nucleic Acids Res , vol.32
    • Torda, A.E.1    Procter, J.B.2    Huber, T.3
  • 60
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein interactions
    • Valencia, A., and Pazos, F. 2002. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12, 368-373.
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 61
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: A protein sequence culling server
    • Wang, G., and Dunbrack, R.L., Jr. 2003. PISCES: a protein sequence culling server. Bioinformatics 19, 1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack, Jr.R.L.2
  • 62
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: A local meta-threading-server for protein structure prediction
    • Wu, S., and Zhang, Y. 2007. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res. 35, 3375-3382.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 63
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • Wu, S., and Zhang, Y. 2008. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 24, 924-931.
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 64
    • 48449085801 scopus 로고    scopus 로고
    • SP5: Improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model
    • Zhang, W., Liu, S., and Zhou, Y. 2008. SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS ONE 3, e2325.
    • (2008) PLoS ONE , vol.3
    • Zhang, W.1    Liu, S.2    Zhou, Y.3
  • 65
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang, Y., and Skolnick, J. 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.