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Volumn 73, Issue 3, 2008, Pages 581-596

Threading without optimizing weighting factors for scoring function

Author keywords

Protein folding; Protein structrure prediction; Scoring function; Threading; Weight optimization

Indexed keywords

ARTICLE; CONSENSUS; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SCORING SYSTEM;

EID: 57349109890     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22082     Document Type: Article
Times cited : (10)

References (73)
  • 1
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: PROSPECTOR - a new approach to threading
    • Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331.
    • (2001) Proteins , vol.42 , pp. 319-331
    • Skolnick, J.1    Kihara, D.2
  • 2
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm
    • Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004;56:502-518.
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 3
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164-170.
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 4
    • 0242720595 scopus 로고    scopus 로고
    • The PDB is a covering set of small protein structures
    • Kihara D, Skolnick J. The PDB is a covering set of small protein structures. J Mol Biol 2003;334:793-802.
    • (2003) J Mol Biol , vol.334 , pp. 793-802
    • Kihara, D.1    Skolnick, J.2
  • 5
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo CA, Jones DT, Thornton JM. Protein superfamilies and domain superfolds. Nature 1994;372:631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 6
    • 30344475200 scopus 로고    scopus 로고
    • Progress over the first decade of CASP experiments
    • Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61 (Suppl):7225-7236.
    • (2005) Proteins , vol.61 , Issue.SUPPL. , pp. 7225-7236
    • Kryshtafovych, A.1    Venclovas, C.2    Fidelis, K.3    Moult, J.4
  • 7
    • 30344449457 scopus 로고    scopus 로고
    • Assessment of fold recognition predictions in CASP6
    • Wang G, Jin Y, Dunbrack RL, Jr. Assessment of fold recognition predictions in CASP6. Proteins 2005;61 (Suppl):746-766.
    • (2005) Proteins , vol.61 , Issue.SUPPL. , pp. 746-766
    • Wang, G.1    Jin, Y.2    Dunbrack Jr., R.L.3
  • 8
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
    • (2000) Protein Sci , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 9
    • 2442663920 scopus 로고    scopus 로고
    • Scoring profile-to-profile sequence alignments
    • Wang G, Dunbrack RL, Jr. Scoring profile-to-profile sequence alignments. Protein Sci 2004;13:1612-1626.
    • (2004) Protein Sci , vol.13 , pp. 1612-1626
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 10
    • 0038278386 scopus 로고    scopus 로고
    • Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry
    • Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry. Proteins 2003;51:504-514.
    • (2003) Proteins , vol.51 , pp. 504-514
    • Karchin, R.1    Cline, M.2    Mandel-Gutfreund, Y.3    Karplus, K.4
  • 11
    • 0032438987 scopus 로고    scopus 로고
    • Hidden Markov models for detecting remote protein homologies
    • Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
    • (1998) Bioinformatics , vol.14 , pp. 846-856
    • Karplus, K.1    Barrett, C.2    Hughey, R.3
  • 12
    • 33744779891 scopus 로고    scopus 로고
    • Sequence comparison and protein structure prediction
    • Dunbrack RL, Jr. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006;16:374-384.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 374-384
    • Dunbrack Jr., R.L.1
  • 13
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • Zhou H, Zhou Y. Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition. Proteins 2004;55:1005-1013.
    • (2004) Proteins , vol.55 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 14
    • 0028579433 scopus 로고
    • Protein structural similarities predicted by a sequence-structure compatibility method
    • Matsuo Y, Nishikawa K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci 1994;3:2055-2063.
    • (1994) Protein Sci , vol.3 , pp. 2055-2063
    • Matsuo, Y.1    Nishikawa, K.2
  • 15
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 16
    • 0031577260 scopus 로고    scopus 로고
    • Protein fold recognition by prediction-based threading
    • Rost B, Schneider R, Sander C. Protein fold recognition by prediction-based threading. J Mol Biol 1997;270:471-480.
    • (1997) J Mol Biol , vol.270 , pp. 471-480
    • Rost, B.1    Schneider, R.2    Sander, C.3
  • 17
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
    • Skolnick J, Jaroszewski L, Kolinski A, Godzik A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci 1997;6:676-688.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 18
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995;5:229-235.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 19
    • 0035964191 scopus 로고    scopus 로고
    • TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints
    • Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 2001;98:10125-10130.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 20
    • 34547620863 scopus 로고    scopus 로고
    • Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
    • Kmiecik S, Gront D, Kolinski A. Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Struct Biol 2007;7:43.
    • (2007) BMC Struct Biol , vol.7 , pp. 43
    • Kmiecik, S.1    Gront, D.2    Kolinski, A.3
  • 21
    • 34548608483 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using chunk-TASSER
    • Zhou H, Skolnick J. Ab initio protein structure prediction using chunk-TASSER. Biophys J 2007;93:1510-1518.
    • (2007) Biophys J , vol.93 , pp. 1510-1518
    • Zhou, H.1    Skolnick, J.2
  • 22
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 23
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: Reranking protein docking predictions with an optimized energy function
    • Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 24
    • 33750056673 scopus 로고    scopus 로고
    • ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
    • Meiler J, Baker D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006;65:538-548.
    • (2006) Proteins , vol.65 , pp. 538-548
    • Meiler, J.1    Baker, D.2
  • 25
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: Current status and future challenges
    • Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: current status and future challenges. Proteins 2006;65:15-26.
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 26
    • 34250829219 scopus 로고    scopus 로고
    • OPUS-Ca: A knowledge-based potential function requiring only Calpha positions
    • Wu Y, Lu M, Chen M, Li J, Ma J. OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci 2007;16:1449-1463.
    • (2007) Protein Sci , vol.16 , pp. 1449-1463
    • Wu, Y.1    Lu, M.2    Chen, M.3    Li, J.4    Ma, J.5
  • 27
    • 33746239564 scopus 로고    scopus 로고
    • Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences
    • Tan YH, Huang H, Kihara D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins 2006;64:587-600.
    • (2006) Proteins , vol.64 , pp. 587-600
    • Tan, Y.H.1    Huang, H.2    Kihara, D.3
  • 28
    • 0031615985 scopus 로고    scopus 로고
    • Linear programming based approach to the derivation of a contact potential for protein threading
    • Akutsu T, Tashimo H. Linear programming based approach to the derivation of a contact potential for protein threading. Pac Symp Biocomput 1998;413-424.
    • (1998) Pac Symp Biocomput , pp. 413-424
    • Akutsu, T.1    Tashimo, H.2
  • 29
    • 0033677331 scopus 로고    scopus 로고
    • A simple iterative approach to parameter optimization
    • Zien A, Zimmer R, Lengauer T. A simple iterative approach to parameter optimization. J Comput Biol 2000;7:483-501.
    • (2000) J Comput Biol , vol.7 , pp. 483-501
    • Zien, A.1    Zimmer, R.2    Lengauer, T.3
  • 30
    • 26944499806 scopus 로고    scopus 로고
    • POEM: Parameter optimization using ensemble methods: application to target specific scoring functions
    • Antes I, Merkwirth C, Lengauer T. POEM: parameter optimization using ensemble methods: application to target specific scoring functions. J Chem Inf Model 2005;45:1291-1302.
    • (2005) J Chem Inf Model , vol.45 , pp. 1291-1302
    • Antes, I.1    Merkwirth, C.2    Lengauer, T.3
  • 31
    • 0033636404 scopus 로고    scopus 로고
    • A method for parameter optimization in computational biology
    • Rosen JB, Phillips AT, Oh SY, Dill KA. A method for parameter optimization in computational biology. Biophys J 2000;79:2818-2824.
    • (2000) Biophys J , vol.79 , pp. 2818-2824
    • Rosen, J.B.1    Phillips, A.T.2    Oh, S.Y.3    Dill, K.A.4
  • 32
    • 0031779709 scopus 로고    scopus 로고
    • Optimizing energy potentials for success in protein tertiary structure prediction
    • Chiu TL, Goldstein RA. Optimizing energy potentials for success in protein tertiary structure prediction. Fold Des 1998;3:223-228.
    • (1998) Fold Des , vol.3 , pp. 223-228
    • Chiu, T.L.1    Goldstein, R.A.2
  • 33
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • Mirny LA, Shakhnovich EI. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 1996;264:1164-1179.
    • (1996) J Mol Biol , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 34
    • 0026785519 scopus 로고
    • Contact potential that recognizes the correct folding of globular proteins
    • Maiorov VN, Crippen GM. Contact potential that recognizes the correct folding of globular proteins. J Mol Biol 1992;227:876-888.
    • (1992) J Mol Biol , vol.227 , pp. 876-888
    • Maiorov, V.N.1    Crippen, G.M.2
  • 35
    • 0029945395 scopus 로고    scopus 로고
    • How optimization of potential functions affects protein folding
    • Hao MH, Scheraga HA. How optimization of potential functions affects protein folding. Proc Natl Acad Sci USA 1996;93:4984-4989.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 4984-4989
    • Hao, M.H.1    Scheraga, H.A.2
  • 36
    • 0037250308 scopus 로고    scopus 로고
    • PDB-REPRDB: A database of representative protein chains from the Protein Data Bank (PDB) in 2003
    • Noguchi T, Akiyama Y. PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. Nucleic Acids Res 2003;31:492-493.
    • (2003) Nucleic Acids Res , vol.31 , pp. 492-493
    • Noguchi, T.1    Akiyama, Y.2
  • 38
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt MR, Thirumalai D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 1999;8:361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 39
    • 0033566614 scopus 로고    scopus 로고
    • An empirical energy potential with a reference state for protein fold and sequence recognition
    • Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999;36:357-369.
    • (1999) Proteins , vol.36 , pp. 357-369
    • Miyazawa, S.1    Jernigan, R.L.2
  • 40
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 41
    • 33646011728 scopus 로고    scopus 로고
    • In quest of an empirical potential for protein structure prediction
    • Skolnick J. In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 2006;16:166-171.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 166-171
    • Skolnick, J.1
  • 42
    • 0033516514 scopus 로고    scopus 로고
    • Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions
    • Huang ES, Samudrala R, Ponder JW. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. J Mol Biol 1999;290:267-281.
    • (1999) J Mol Biol , vol.290 , pp. 267-281
    • Huang, E.S.1    Samudrala, R.2    Ponder, J.W.3
  • 43
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507-2524.
    • (2006) Protein Sci , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 44
    • 40549141792 scopus 로고    scopus 로고
    • QMEAN: A comprehensive scoring function for model quality assessment
    • Benkert P, Tosatto SC, Schomburg D. QMEAN: a comprehensive scoring function for model quality assessment. Proteins 2008;71:261-277.
    • (2008) Proteins , vol.71 , pp. 261-277
    • Benkert, P.1    Tosatto, S.C.2    Schomburg, D.3
  • 45
    • 0027180507 scopus 로고
    • Verification of protein structures: Patterns of nonbonded atomic interactions
    • Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 1993;2:1511-1519.
    • (1993) Protein Sci , vol.2 , pp. 1511-1519
    • Colovos, C.1    Yeates, T.O.2
  • 46
    • 0031582083 scopus 로고    scopus 로고
    • Novel knowledge-based mean force potential at atomic level
    • Melo F, Feytmans E. Novel knowledge-based mean force potential at atomic level. J Mol Biol 1997;267:207-222.
    • (1997) J Mol Biol , vol.267 , pp. 207-222
    • Melo, F.1    Feytmans, E.2
  • 47
    • 33646786723 scopus 로고    scopus 로고
    • Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors
    • Zhang J, Chen R, Liang J. Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors. Proteins 2006;63:949-960.
    • (2006) Proteins , vol.63 , pp. 949-960
    • Zhang, J.1    Chen, R.2    Liang, J.3
  • 48
    • 16344387893 scopus 로고    scopus 로고
    • A new approach to prediction of short-range conformational propensities in proteins
    • Gront D, Kolinski A. A new approach to prediction of short-range conformational propensities in proteins. Bioinformatics 2005;21:981-987.
    • (2005) Bioinformatics , vol.21 , pp. 981-987
    • Gront, D.1    Kolinski, A.2
  • 49
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001;44:223-232.
    • (2001) Proteins , vol.44 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 50
    • 0345411953 scopus 로고    scopus 로고
    • A reduced protein model with accurate native-structure identification ability
    • Betancourt MR. A reduced protein model with accurate native-structure identification ability. Proteins 2003;53:889-907.
    • (2003) Proteins , vol.53 , pp. 889-907
    • Betancourt, M.R.1
  • 51
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • Tobi D, Elber R. Distance-dependent, pair potential for protein folding: results from linear optimization. Proteins 2000;41:40-46.
    • (2000) Proteins , vol.41 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 52
    • 0000939821 scopus 로고    scopus 로고
    • What is the probability of a chance prediction of a protein structure with an rmsd of 6 A?
    • Reva BA, Finkelstein AV, Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Fold Des 1998;3:141-147.
    • (1998) Fold Des , vol.3 , pp. 141-147
    • Reva, B.A.1    Finkelstein, A.V.2    Skolnick, J.3
  • 54
    • 2942689229 scopus 로고    scopus 로고
    • Prediction of protein folding rates from the amino acid sequence-predicted secondary structure
    • Ivankov DN, Finkelstein AV. Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc Natl Acad Sci USA 2004;101:8942-8944.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 8942-8944
    • Ivankov, D.N.1    Finkelstein, A.V.2
  • 55
    • 0022631926 scopus 로고
    • The folding type of a protein is relevant to the amino acid composition
    • Nakashima H, Nishikawa K, Ooi T. The folding type of a protein is relevant to the amino acid composition. J Biochem (Tokyo) 1986;99:153-162.
    • (1986) J Biochem (Tokyo) , vol.99 , pp. 153-162
    • Nakashima, H.1    Nishikawa, K.2    Ooi, T.3
  • 56
    • 0022777472 scopus 로고
    • Prediction of protein structural class from the amino acid sequence
    • Klein P, DeLisi C. Prediction of protein structural class from the amino acid sequence. Biopolymers 1986;25:1659-1672.
    • (1986) Biopolymers , vol.25 , pp. 1659-1672
    • Klein, P.1    DeLisi, C.2
  • 57
    • 26844545834 scopus 로고    scopus 로고
    • Progress in protein structural class prediction and its impact to bioinformatics and proteomics
    • Chou KC. Progress in protein structural class prediction and its impact to bioinformatics and proteomics. Curr Protein Pept Sci 2005;6:423-436.
    • (2005) Curr Protein Pept Sci , vol.6 , pp. 423-436
    • Chou, K.C.1
  • 58
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005;59:467-475.
    • (2005) Proteins , vol.59 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 60
    • 4344697167 scopus 로고    scopus 로고
    • Local propensities and statistical potentials of backbone dihedral angles in proteins
    • Betancourt MR, Skolnick J. Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol 2004;342:635-649.
    • (2004) J Mol Biol , vol.342 , pp. 635-649
    • Betancourt, M.R.1    Skolnick, J.2
  • 61
    • 33746486702 scopus 로고    scopus 로고
    • Secondary structure determines protein topology
    • Fleming PJ, Gong H, Rose GD. Secondary structure determines protein topology. Protein Sci 2006;15:1829-1834.
    • (2006) Protein Sci , vol.15 , pp. 1829-1834
    • Fleming, P.J.1    Gong, H.2    Rose, G.D.3
  • 62
    • 23644456329 scopus 로고    scopus 로고
    • The effect of long-range interactions on the secondary structure formation of proteins
    • Kihara D. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 2005;14:1955-1963.
    • (2005) Protein Sci , vol.14 , pp. 1955-1963
    • Kihara, D.1
  • 65
    • 33750210515 scopus 로고    scopus 로고
    • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection
    • Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res 2006;34:e112.
    • (2006) Nucleic Acids Res , vol.34
    • Chivian, D.1    Baker, D.2
  • 66
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHOTGUN: A novel, cooperative, fold-recognition meta-predictor
    • Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 2003;51:434-441.
    • (2003) Proteins , vol.51 , pp. 434-441
    • Fischer, D.1
  • 67
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
    • (2003) Bioinformatics , vol.19 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 68
    • 33847107996 scopus 로고    scopus 로고
    • EMD: An ensemble algorithm for discovering regulatory motifs in DNA sequences
    • Hu J, Yang YD, Kihara D. EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences. BMC Bioinformatics 2006;7:342.
    • (2006) BMC Bioinformatics , vol.7 , pp. 342
    • Hu, J.1    Yang, Y.D.2    Kihara, D.3
  • 69
    • 0037414421 scopus 로고    scopus 로고
    • In silico protein recombination: Enhancing template and sequence alignment selection for comparative protein modelling
    • Contreras-Moreira B, Fitzjohn PW, Bates PA. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. J Mol Biol 2003;328:593-608.
    • (2003) J Mol Biol , vol.328 , pp. 593-608
    • Contreras-Moreira, B.1    Fitzjohn, P.W.2    Bates, P.A.3
  • 70
    • 28444454499 scopus 로고    scopus 로고
    • Pcons5: Combining consensus, structural evaluation and fold recognition scores
    • Wallner B, Elofsson A. Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 2005;21:4248-4254.
    • (2005) Bioinformatics , vol.21 , pp. 4248-4254
    • Wallner, B.1    Elofsson, A.2
  • 71
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000;302:205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 72
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol 1997;4:10-19.
    • (1997) Nat Struct Biol , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 73
    • 0035874127 scopus 로고    scopus 로고
    • Population analyses of kinetic partitioning in protein folding
    • Nakamura HK, Sasai M. Population analyses of kinetic partitioning in protein folding. Proteins 2001;43:280-291.
    • (2001) Proteins , vol.43 , pp. 280-291
    • Nakamura, H.K.1    Sasai, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.