메뉴 건너뛰기




Volumn 5, Issue 21, 2008, Pages 387-396

A comparative study of the reported performance of ab initio protein structure prediction algorithms

Author keywords

ab initio; Algorithms; De novo; Performance; Protein structure prediction

Indexed keywords

ALGORITHMS; BIOINFORMATICS; COMPUTATIONAL EFFICIENCY; MOLECULAR STRUCTURE; RESPONSE TIME (COMPUTER SYSTEMS);

EID: 39149143625     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2007.1278     Document Type: Review
Times cited : (53)

References (44)
  • 1
    • 33344457736 scopus 로고    scopus 로고
    • Protein structure prediction using mutually orthogonal latin squares and a genetic algorithm
    • doi:10.1016/j.bbrc. 2006.01.162
    • Arunachalam, J., Kanagasabai, V. & Gautham, N. 2006 Protein structure prediction using mutually orthogonal latin squares and a genetic algorithm. Biochem. Biophys. Res. Commun. 342, 424-433. (doi:10.1016/j.bbrc. 2006.01.162)
    • (2006) Biochem. Biophys. Res. Commun , vol.342 , pp. 424-433
    • Arunachalam, J.1    Kanagasabai, V.2    Gautham, N.3
  • 3
    • 24944493938 scopus 로고    scopus 로고
    • Towards high-resolution de novo structure prediction for small proteins
    • doi:10.1126/science.1113801
    • Bradley, P., Misura, K. M. S. & Baker, D. 2005b Towards high-resolution de novo structure prediction for small proteins. Science 309, 1868-1871. (doi:10.1126/science.1113801)
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 4
    • 23144464777 scopus 로고    scopus 로고
    • Hidden Markov model-derived structural alphabet for proteins: The learning of protein local shapes captures sequence specificity
    • Camproux, A. C. & Tuffery, P. 2005 Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity. Biochim. Biophys. Acta 1724, 394-403.
    • (2005) Biochim. Biophys. Acta , vol.1724 , pp. 394-403
    • Camproux, A.C.1    Tuffery, P.2
  • 5
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • doi:10.1110/ps.690101
    • Carugo, O. & Pongor, S. 2001 A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci. 10, 1470-1473. (doi:10.1110/ps.690101)
    • (2001) Protein Sci , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 6
    • 33747089280 scopus 로고    scopus 로고
    • A multi-objective evolutionary approach to the protein structure prediction problem
    • doi:10.1098/rsif.2005.0083
    • Cutello, V., Narzisi, G. & Nicosia, G. 2006 A multi-objective evolutionary approach to the protein structure prediction problem. J. R. Soc. Interface 3, 139-151. (doi:10.1098/rsif.2005.0083)
    • (2006) J. R. Soc. Interface , vol.3 , pp. 139-151
    • Cutello, V.1    Narzisi, G.2    Nicosia, G.3
  • 7
    • 34250893049 scopus 로고    scopus 로고
    • Effective optimization algorithms for fragment-assembly based protein structure prediction
    • Stanford, CA, USA, pp, London, UK: Imperial College Press
    • DeRonne, K. W. & Karypis, G. 2006 Effective optimization algorithms for fragment-assembly based protein structure prediction. In Computational Systems Bioinformatics Conference, Stanford, CA, USA, pp. 19-29. London, UK: Imperial College Press.
    • (2006) Computational Systems Bioinformatics Conference , pp. 19-29
    • DeRonne, K.W.1    Karypis, G.2
  • 8
    • 0036667731 scopus 로고    scopus 로고
    • Rotamer libraries in the 21st century
    • doi:10.1016/S0959-440X(02)00344-5
    • Dunbrack, R. L. 2002 Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12, 431-440. (doi:10.1016/S0959-440X(02)00344-5)
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 431-440
    • Dunbrack, R.L.1
  • 9
    • 0037323213 scopus 로고    scopus 로고
    • Bioinformatics methods to predict protein structure and function
    • doi:10.1385/MB:23:2:139
    • Edwards, Y. J. K. & Cottage, A. 2003 Bioinformatics methods to predict protein structure and function. Mol. Biotechnol. 23, 139-166. (doi:10.1385/MB:23:2:139)
    • (2003) Mol. Biotechnol , vol.23 , pp. 139-166
    • Edwards, Y.J.K.1    Cottage, A.2
  • 10
    • 33847356936 scopus 로고    scopus 로고
    • A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction
    • doi:10.1002/prot. 21223
    • Eyal, ., Frenkel-Morgenstern, M., Sobolev, V. & Pietrokovski, S. 2007 A pair-to-pair amino acids substitution matrix and its applications for protein structure prediction. Proteins 67, 142-153. (doi:10.1002/prot. 21223)
    • (2007) Proteins , vol.67 , pp. 142-153
    • Eyal1    Frenkel-Morgenstern, M.2    Sobolev, V.3    Pietrokovski, S.4
  • 11
    • 30144441768 scopus 로고    scopus 로고
    • SimFold energy function for de novo protein structure prediction: Consensus with Rosetta
    • doi:10.1002/prot.20748
    • Fujitsuka, Y., Chikenji, G. & Takada, S. 2006 SimFold energy function for de novo protein structure prediction: consensus with Rosetta. Proteins 62, 381-398. (doi:10.1002/prot.20748)
    • (2006) Proteins , vol.62 , pp. 381-398
    • Fujitsuka, Y.1    Chikenji, G.2    Takada, S.3
  • 12
    • 0034275016 scopus 로고    scopus 로고
    • Comparison of three Monte Carlo conformational search strategies for a protein like homopolymer model: Folding thermodynamics and identification of low-energy structures
    • doi:10.1063/1.1289533
    • Gront, D., Kolinski, A. & Skolnick, J. 2000 Comparison of three Monte Carlo conformational search strategies for a protein like homopolymer model: folding thermodynamics and identification of low-energy structures. J. Chem. Phys. 113, 5065-5071. (doi:10.1063/1.1289533)
    • (2000) J. Chem. Phys , vol.113 , pp. 5065-5071
    • Gront, D.1    Kolinski, A.2    Skolnick, J.3
  • 13
    • 33847636089 scopus 로고    scopus 로고
    • Guo, Y. Z., Feng, E. M. & Wang, Y. 2007 Optimal HP configurations of proteins by combining local search with elastic net algorithm. J. Biochem. Biophys. Methods 70, 335-340. (doi:10.1016/j.jbbm.2006.08.001)
    • Guo, Y. Z., Feng, E. M. & Wang, Y. 2007 Optimal HP configurations of proteins by combining local search with elastic net algorithm. J. Biochem. Biophys. Methods 70, 335-340. (doi:10.1016/j.jbbm.2006.08.001)
  • 14
    • 0036535974 scopus 로고    scopus 로고
    • Ab initio protein structure prediction
    • doi:10.1016/S0959-440X(02)00306-8
    • Hardin, C., Pogorelov, T. V. & Luthey-Schulten, Z. 2002 Ab initio protein structure prediction. Curr. Opin. Struct. Biol. 12, 176-181. (doi:10.1016/S0959-440X(02)00306-8)
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 176-181
    • Hardin, C.1    Pogorelov, T.V.2    Luthey-Schulten, Z.3
  • 15
    • 33845611519 scopus 로고    scopus 로고
    • Routes are trees: The parsing perspective on protein folding
    • doi:10.1002/prot.21195
    • Hockenmaier, J., Joshi, A. K. & Dill, K. A. 2007 Routes are trees: the parsing perspective on protein folding. Proteins 66, 1-15. (doi:10.1002/prot.21195)
    • (2007) Proteins , vol.66 , pp. 1-15
    • Hockenmaier, J.1    Joshi, A.K.2    Dill, K.A.3
  • 16
    • 21444448763 scopus 로고    scopus 로고
    • PROTINFO: New algorithms for enhanced protein structure predictions
    • doi:10.1093/nar/gki403
    • Hung, L., Ngan, S., Liu, T. & Samudrala, R. 2005 PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res. 33, W77-W80. (doi:10.1093/nar/gki403)
    • (2005) Nucleic Acids Res , vol.33
    • Hung, L.1    Ngan, S.2    Liu, T.3    Samudrala, R.4
  • 17
    • 36749086922 scopus 로고    scopus 로고
    • Assessment of CASP7 structure predictions for template free targets
    • doi:10.1002/prot.21771
    • Jauch, R., Yeo, H. C., Kolatkar, P. R. & Clarke, N. D. 2007 Assessment of CASP7 structure predictions for template free targets. Proteins: Struct. Funct. Bioinform. 66, 57-67. (doi:10.1002/prot.21771)
    • (2007) Proteins: Struct. Funct. Bioinform , vol.66 , pp. 57-67
    • Jauch, R.1    Yeo, H.C.2    Kolatkar, P.R.3    Clarke, N.D.4
  • 18
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • doi:10.1006/jmbi.1999.3091
    • Jones, D. T. 1999 Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202. (doi:10.1006/jmbi.1999.3091)
    • (1999) J. Mol. Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 20
    • 0042229154 scopus 로고    scopus 로고
    • Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm
    • doi:10.1016/S0097-8485(02)00074-8
    • Joshi, R. R. & Jyothi, S. 2003 Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm. Comput. Biol. Chem. 27, 241-252. (doi:10.1016/S0097-8485(02)00074-8)
    • (2003) Comput. Biol. Chem , vol.27 , pp. 241-252
    • Joshi, R.R.1    Jyothi, S.2
  • 21
    • 0141642142 scopus 로고    scopus 로고
    • ASTRO-FOLD: A combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
    • Klepeis, J. L. & Floudas, C. A. 2003 ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys. J. 85, 2119-2146.
    • (2003) Biophys. J , vol.85 , pp. 2119-2146
    • Klepeis, J.L.1    Floudas, C.A.2
  • 22
    • 3242779291 scopus 로고    scopus 로고
    • Protein modeling and structure prediction with a reduced representation
    • Kolinski, A. 2004 Protein modeling and structure prediction with a reduced representation. Acta Biochim. Polon. 51, 349-371.
    • (2004) Acta Biochim. Polon , vol.51 , pp. 349-371
    • Kolinski, A.1
  • 23
    • 22844445557 scopus 로고    scopus 로고
    • Towards protein folding with evolutionary techniques
    • doi:10.1002/jcc.20254
    • Koskowski, F. & Hartke, B. 2004 Towards protein folding with evolutionary techniques. J. Comput. Chem. 26, 1169-1179. (doi:10.1002/jcc.20254)
    • (2004) J. Comput. Chem , vol.26 , pp. 1169-1179
    • Koskowski, F.1    Hartke, B.2
  • 25
    • 0033514939 scopus 로고    scopus 로고
    • Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
    • doi:10.1073/pnas.96.5.2025
    • Lee, J., Liwo, A. & Scheraga, H. A. 1999 Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K. Proc. Natl Acad. Sci. USA 96, 2025-2030. (doi:10.1073/pnas.96.5.2025)
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 2025-2030
    • Lee, J.1    Liwo, A.2    Scheraga, H.A.3
  • 26
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
    • doi:10.1002/prot.20150
    • Lee, J., Kim, S.-Y., Joo, K., Kim, I. & Lee, J. 2004 Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing. Proteins: Struct. Funct. Bioinform. 56, 704-714. (doi:10.1002/prot.20150)
    • (2004) Proteins: Struct. Funct. Bioinform , vol.56 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 27
    • 14744276882 scopus 로고    scopus 로고
    • Protein structure prediction based on fragment assembly and parameter optimization
    • doi:10.1016/j.bpc.2004.12.046
    • Lee, J., Kim, S.-Y. & Lee, J. 2005 Protein structure prediction based on fragment assembly and parameter optimization. Biophys. Chem. 115, 209-214. (doi:10.1016/j.bpc.2004.12.046)
    • (2005) Biophys. Chem , vol.115 , pp. 209-214
    • Lee, J.1    Kim, S.-Y.2    Lee, J.3
  • 28
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • doi:10.1073/pnas.0408885102
    • Liwo, A., Khalili, M. & Scheraga, H. A. 2005 Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl Acad. Sci. USA 102, 2362-2367. (doi:10.1073/pnas.0408885102)
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 29
    • 24944485477 scopus 로고    scopus 로고
    • Unique optimal foldings of proteins on a triangular lattice
    • doi:10.2165/00822942-200504020-00004
    • Li, Z., Zhang, X. & Chen, L. 2005 Unique optimal foldings of proteins on a triangular lattice. Appl. Bioinform. 4, 105-116. (doi:10.2165/00822942-200504020-00004)
    • (2005) Appl. Bioinform , vol.4 , pp. 105-116
    • Li, Z.1    Zhang, X.2    Chen, L.3
  • 30
    • 4444351490 scopus 로고    scopus 로고
    • Empirical force fields for biological macromolecules: Overview and issues
    • doi:10.1002/jcc.20082
    • MacKerell Jr, A. D. 2004 Empirical force fields for biological macromolecules: overview and issues. J. Comput. Chem. 25, 1584-1604. (doi:10.1002/jcc.20082)
    • (2004) J. Comput. Chem , vol.25 , pp. 1584-1604
    • MacKerell Jr, A.D.1
  • 31
    • 0030777303 scopus 로고    scopus 로고
    • CATH-a hierarchic classification of protein domain structures
    • doi:10.1016/S0969-2126(97) 00260-8
    • Orengo, C. A., ichie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. 1997 CATH-a hierarchic classification of protein domain structures. Structure 5, 1093-1108. (doi:10.1016/S0969-2126(97) 00260-8)
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.A.1    ichie, A.D.2    Jones, S.3    Jones, D.T.4    Swindells, M.B.5    Thornton, J.M.6
  • 32
    • 34547551805 scopus 로고    scopus 로고
    • Protein folding by zipping and assembly
    • doi:10.1073/pnas.0703700104
    • Ozkan, S. B., Wu, G. A., Chodera, J. D. & Dill, K. A. 2007 Protein folding by zipping and assembly. Proc. Natl Acad. Sci. USA 104, 11 987-11 992. (doi:10.1073/pnas.0703700104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104
    • Ozkan, S.B.1    Wu, G.A.2    Chodera, J.D.3    Dill, K.A.4
  • 33
    • 0014381393 scopus 로고
    • Conformation of polypeptides and proteins
    • Ramachandran, . N. & Sasisekharan, V. 1968 Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283-438.
    • (1968) Adv. Protein Chem , vol.23 , pp. 283-438
    • Ramachandran, N.1    Sasisekharan, V.2
  • 34
    • 0000939821 scopus 로고    scopus 로고
    • What is the probability of a chance prediction of a protein structure with an RMSD of 6 å?
    • doi:10.1016/S1359-0278(98)00019-4
    • Reva, B. A., Finkelstein, A. V. & Skolnick, J. 1998 What is the probability of a chance prediction of a protein structure with an RMSD of 6 å? Fold des 3, 141-147. (doi:10.1016/S1359-0278(98)00019-4)
    • (1998) Fold des , vol.3 , pp. 141-147
    • Reva, B.A.1    Finkelstein, A.V.2    Skolnick, J.3
  • 35
    • 1642464839 scopus 로고    scopus 로고
    • Protein structure prediction using rosetta
    • doi:10.1016/S1359-0278(98)00019-4
    • Rohl, C. A., Strauss, C. E. M., Misura, K. M. S. & Baker, D. 2004 Protein structure prediction using rosetta. Methods Enzymol. 383, 66-93. (doi:10.1016/S1359-0278(98)00019-4)
    • (2004) Methods Enzymol , vol.383 , pp. 66-93
    • Rohl, C.A.1    Strauss, C.E.M.2    Misura, K.M.S.3    Baker, D.4
  • 36
    • 85020794573 scopus 로고    scopus 로고
    • Samudrala, R. 1990 Genes, macromolecules & computers. See http://www.ram.org/ramblings/dream/.
    • Samudrala, R. 1990 Genes, macromolecules & computers. See http://www.ram.org/ramblings/dream/.
  • 37
    • 33744816177 scopus 로고    scopus 로고
    • An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein L20
    • doi:10.1529/biophysj.105.070409
    • Schug, A. & Wenzel, W. 2006 An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein L20. Biophys. J. 90, 4273-4280. (doi:10.1529/biophysj.105.070409)
    • (2006) Biophys. J , vol.90 , pp. 4273-4280
    • Schug, A.1    Wenzel, W.2
  • 38
    • 33646011728 scopus 로고    scopus 로고
    • In quest of an empirical potential for protein structure prediction
    • doi:10.1016/j.sbi.2006.02.004
    • Skolnick, J. 2006 In quest of an empirical potential for protein structure prediction. Curr. Opin. Struct. Biol. 16, 166-171. (doi:10.1016/j.sbi.2006.02.004)
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 166-171
    • Skolnick, J.1
  • 39
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • doi:10.1186/1741-7007-5-17
    • Wu, S., Skolnick, J. & Zhang, Y. 2007 Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 5, 17. (doi:10.1186/1741-7007-5-17)
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 40
    • 33846104376 scopus 로고    scopus 로고
    • All-atom ab initio folding of a diverse set of proteins
    • doi:10.1016/j.str.2006.11.010
    • Yang, J. S., Chen, W. W., Skolnick, J. & Shakhnovich, E. I. 2006 All-atom ab initio folding of a diverse set of proteins. Structure 15, 53-63. (doi:10.1016/j.str.2006.11.010)
    • (2006) Structure , vol.15 , pp. 53-63
    • Yang, J.S.1    Chen, W.W.2    Skolnick, J.3    Shakhnovich, E.I.4
  • 41
    • 0036428782 scopus 로고    scopus 로고
    • Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
    • doi:10.1016/S0022-2836(02)00997-X
    • Zagrovic, B., Snow, C. D., Shirts, M. R. & Pande, V. S. 2002 Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323, 927-937. (doi:10.1016/S0022-2836(02)00997-X)
    • (2002) J. Mol. Biol , vol.323 , pp. 927-937
    • Zagrovic, B.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 42
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • doi:10.1073/pnas.0407152101
    • Zhang, Y. & Skolnick, J. 2004 The protein structure prediction problem could be solved using the current PDB library. Proc. Natl Acad. Sci. USA 102, 1029-1034. (doi:10.1073/pnas.0407152101)
    • (2004) Proc. Natl Acad. Sci. USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2
  • 43
    • 0041843696 scopus 로고    scopus 로고
    • TOUCHSTONE II: A new approach to ab initio protein structure prediction
    • Zhang, Y., Kolinski, A. & Skolnick, J. 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
  • 44
    • 34548608483 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using chunk-TASSER
    • doi:10.1529/biophysj.107.109959
    • Zhou, H. & Skolnick, J. 2007 Ab initio protein structure prediction using chunk-TASSER. Biophys. J. 93, 1510-1518. (doi:10.1529/biophysj.107.109959)
    • (2007) Biophys. J , vol.93 , pp. 1510-1518
    • Zhou, H.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.