메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

Effective inter-residue contact definitions for accurate protein fold recognition

Author keywords

Fold recognition; Protein fold; Protein structure prediction; Residue residue contact; Structural features; Threading

Indexed keywords

FOLD RECOGNITION; PROTEIN FOLDS; PROTEIN STRUCTURE PREDICTION; STRUCTURAL FEATURE; THREADING;

EID: 84868558712     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-292     Document Type: Article
Times cited : (43)

References (48)
  • 1
    • 3242813635 scopus 로고    scopus 로고
    • Utility of homology models in the drug discovery process
    • 10.1016/S1359-6446(04)03196-4, 15279849
    • Hillisch A, Pineda LF, Hilgenfeld R. Utility of homology models in the drug discovery process. Drug Discov Today 2004, 9:659-669. 10.1016/S1359-6446(04)03196-4, 15279849.
    • (2004) Drug Discov Today , vol.9 , pp. 659-669
    • Hillisch, A.1    Pineda, L.F.2    Hilgenfeld, R.3
  • 2
    • 1642345577 scopus 로고    scopus 로고
    • Protein structure prediction in structure based drug design
    • 10.2174/0929867043455837, 15032603
    • Takeda-Shitaka M, Takaya D, Chiba C, Tanaka H, Umeyama H. Protein structure prediction in structure based drug design. Curr Med Chem 2004, 11:551-558. 10.2174/0929867043455837, 15032603.
    • (2004) Curr Med Chem , vol.11 , pp. 551-558
    • Takeda-Shitaka, M.1    Takaya, D.2    Chiba, C.3    Tanaka, H.4    Umeyama, H.5
  • 3
    • 33745278855 scopus 로고    scopus 로고
    • Computational redesign of endonuclease DNA binding and cleavage specificity
    • 10.1038/nature04818, 2999987, 16738662
    • Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 2006, 441:656-659. 10.1038/nature04818, 2999987, 16738662.
    • (2006) Nature , vol.441 , pp. 656-659
    • Ashworth, J.1    Havranek, J.J.2    Duarte, C.M.3    Sussman, D.4    Monnat, R.J.5    Stoddard, B.L.6    Baker, D.7
  • 5
    • 79958003499 scopus 로고    scopus 로고
    • Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins
    • 10.1016/j.cbpa.2011.03.014, 21493122
    • Saven JG. Computational protein design: engineering molecular diversity, nonnatural enzymes, nonbiological cofactor complexes, and membrane proteins. Curr Opin Chem Biol 2011, 15:452-457. 10.1016/j.cbpa.2011.03.014, 21493122.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 452-457
    • Saven, J.G.1
  • 6
    • 52949096084 scopus 로고    scopus 로고
    • Next-generation DNA sequencing methods
    • 10.1146/annurev.genom.9.081307.164359, 18576944
    • Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008, 9:387-402. 10.1146/annurev.genom.9.081307.164359, 18576944.
    • (2008) Annu Rev Genomics Hum Genet , vol.9 , pp. 387-402
    • Mardis, E.R.1
  • 7
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • 10.1038/nrg2626, 19997069
    • Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
    • (2010) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 10
    • 1842479856 scopus 로고    scopus 로고
    • Microbial Genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q
    • 10.1002/prot.20044, 15048836
    • Kihara D, Skolnick J. Microbial Genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins 2004, 55:464-473. 10.1002/prot.20044, 15048836.
    • (2004) Proteins , vol.55 , pp. 464-473
    • Kihara, D.1    Skolnick, J.2
  • 11
    • 44949145113 scopus 로고    scopus 로고
    • Progress and challenges in protein structure prediction
    • 10.1016/j.sbi.2008.02.004, 2680823, 18436442
    • Zhang Y. Progress and challenges in protein structure prediction. Curr Opin Struct Biol 2008, 18:342-348. 10.1016/j.sbi.2008.02.004, 2680823, 18436442.
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 342-348
    • Zhang, Y.1
  • 12
    • 78649797219 scopus 로고    scopus 로고
    • Effect of using suboptimal alignments in template-based protein structure prediction
    • 10.1002/prot.22885, 3058269, 21058297
    • Chen H, Kihara D. Effect of using suboptimal alignments in template-based protein structure prediction. Proteins 2011, 79:315-334. 10.1002/prot.22885, 3058269, 21058297.
    • (2011) Proteins , vol.79 , pp. 315-334
    • Chen, H.1    Kihara, D.2
  • 13
    • 80855133462 scopus 로고    scopus 로고
    • CASP9 assessment of free modeling target predictions
    • 3226891, 21997521
    • Kinch L, Yong SS, Cong Q, Cheng H, Liao Y, Grishin NV. CASP9 assessment of free modeling target predictions. Proteins 2011, 79(Suppl 10):59-73. 3226891, 21997521.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 59-73
    • Kinch, L.1    Yong, S.S.2    Cong, Q.3    Cheng, H.4    Liao, Y.5    Grishin, N.V.6
  • 14
    • 69449098446 scopus 로고    scopus 로고
    • A guide to template based structure prediction
    • 10.2174/138920309788452182, 19519455
    • Qu X, Swanson R, Day R, Tsai J. A guide to template based structure prediction. Curr Protein Pept Sci 2009, 10:270-285. 10.2174/138920309788452182, 19519455.
    • (2009) Curr Protein Pept Sci , vol.10 , pp. 270-285
    • Qu, X.1    Swanson, R.2    Day, R.3    Tsai, J.4
  • 15
    • 34447506573 scopus 로고    scopus 로고
    • Fold recognition by concurrent use of solvent accessibility and residue depth
    • 10.1002/prot.21459, 17510969
    • Liu S, Zhang C, Liang S, Zhou Y. Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins 2007, 68:636-645. 10.1002/prot.21459, 17510969.
    • (2007) Proteins , vol.68 , pp. 636-645
    • Liu, S.1    Zhang, C.2    Liang, S.3    Zhou, Y.4
  • 16
    • 2542631929 scopus 로고    scopus 로고
    • Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition
    • 10.1002/prot.20007, 15146497
    • 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. 10.1002/prot.20007, 15146497.
    • (2004) Proteins , vol.55 , pp. 1005-1013
    • Zhou, H.1    Zhou, Y.2
  • 17
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: PROSPECTOR-a new approach to threading
    • 10.1002/1097-0134(20010215)42:3<319::AID-PROT30>3.0.CO;2-A, 11151004
    • Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR-a new approach to threading. Proteins 2001, 42:319-331. 10.1002/1097-0134(20010215)42:3<319::AID-PROT30>3.0.CO;2-A, 11151004.
    • (2001) Proteins , vol.42 , pp. 319-331
    • Skolnick, J.1    Kihara, D.2
  • 18
    • 3142764482 scopus 로고    scopus 로고
    • Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm
    • 10.1002/prot.20106, 15229883
    • Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Proteins 2004, 56:502-518. 10.1002/prot.20106, 15229883.
    • (2004) Proteins , vol.56 , pp. 502-518
    • Skolnick, J.1    Kihara, D.2    Zhang, Y.3
  • 19
    • 17844392864 scopus 로고    scopus 로고
    • Combining prediction of secondary structure and solvent accessibility in proteins
    • 10.1002/prot.20441, 15768403
    • Adamczak R, Porollo A, Meller J. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 2005, 59:467-475. 10.1002/prot.20441, 15768403.
    • (2005) Proteins , vol.59 , pp. 467-475
    • Adamczak, R.1    Porollo, A.2    Meller, J.3
  • 20
    • 84871725918 scopus 로고    scopus 로고
    • Protein structure prediction without optimizing weighting factors for scoring function
    • Yang YD, Park C, Kihara D. Protein structure prediction without optimizing weighting factors for scoring function. Biophys J 2009, 96:653a.
    • (2009) Biophys J , vol.96
    • Yang, Y.D.1    Park, C.2    Kihara, D.3
  • 21
    • 0029000696 scopus 로고
    • Knowledge-based potentials for proteins
    • 10.1016/0959-440X(95)80081-6, 7648326
    • Sippl MJ. Knowledge-based potentials for proteins. Curr Opin Struct Biol 1995, 5:229-235. 10.1016/0959-440X(95)80081-6, 7648326.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 229-235
    • Sippl, M.J.1
  • 22
    • 0030983768 scopus 로고    scopus 로고
    • Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct
    • 2143667, 9070450
    • 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. 2143667, 9070450.
    • (1997) Protein Sci , vol.6 , pp. 676-688
    • Skolnick, J.1    Jaroszewski, L.2    Kolinski, A.3    Godzik, A.4
  • 23
    • 80054694711 scopus 로고    scopus 로고
    • GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
    • 10.1016/j.bpj.2011.09.012, 3192975, 22004759
    • Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 2011, 101:2043-2052. 10.1016/j.bpj.2011.09.012, 3192975, 22004759.
    • (2011) Biophys J , vol.101 , pp. 2043-2052
    • Zhou, H.1    Skolnick, J.2
  • 24
    • 23644456329 scopus 로고    scopus 로고
    • The effect of long-range interactions on the secondary structure formation of proteins
    • 10.1110/ps.051479505, 2279307, 15987894
    • Kihara D. The effect of long-range interactions on the secondary structure formation of proteins. Protein Sci 2005, 14:1955-1963. 10.1110/ps.051479505, 2279307, 15987894.
    • (2005) Protein Sci , vol.14 , pp. 1955-1963
    • Kihara, D.1
  • 25
    • 0016696599 scopus 로고
    • Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions
    • Taketomi H, Ueda Y, Go N. Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. Int J Pept Protein Res 1975, 7:445-459.
    • (1975) Int J Pept Protein Res , vol.7 , pp. 445-459
    • Taketomi, H.1    Ueda, Y.2    Go, N.3
  • 26
    • 78651323643 scopus 로고    scopus 로고
    • Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure
    • 10.1186/1756-0381-4-1, 3033854, 21232136
    • Vassura M, Di LP, Margara L, Mirto M, Aloisio G, Fariselli P, Casadio R. Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure. BioData Min 2011, 4:1. 10.1186/1756-0381-4-1, 3033854, 21232136.
    • (2011) BioData Min , vol.4 , pp. 1
    • Vassura, M.1    Di, L.P.2    Margara, L.3    Mirto, M.4    Aloisio, G.5    Fariselli, P.6    Casadio, R.7
  • 27
    • 77952705908 scopus 로고    scopus 로고
    • Optimal contact definition for reconstruction of contact maps
    • 10.1186/1471-2105-11-283, 20507547
    • Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M. Optimal contact definition for reconstruction of contact maps. BMC Bioinformatics 2010, 11:283. 10.1186/1471-2105-11-283, 20507547.
    • (2010) BMC Bioinformatics , vol.11 , pp. 283
    • Duarte, J.M.1    Sathyapriya, R.2    Stehr, H.3    Filippis, I.4    Lappe, M.5
  • 28
    • 0030627407 scopus 로고    scopus 로고
    • Recovery of protein structure from contact maps
    • 10.1016/S1359-0278(97)00041-2, 9377713
    • Vendruscolo M, Kussell E, Domany E. Recovery of protein structure from contact maps. Fold Des 1997, 2:295-306. 10.1016/S1359-0278(97)00041-2, 9377713.
    • (1997) Fold Des , vol.2 , pp. 295-306
    • Vendruscolo, M.1    Kussell, E.2    Domany, E.3
  • 30
    • 0028557303 scopus 로고
    • Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds
    • 10.1002/pro.5560031221, 2142768, 7756991
    • Rodionov MA, Johnson MS. Residue-residue contact substitution probabilities derived from aligned three-dimensional structures and the identification of common folds. Protein Sci 1994, 3:2366-2377. 10.1002/pro.5560031221, 2142768, 7756991.
    • (1994) Protein Sci , vol.3 , pp. 2366-2377
    • Rodionov, M.A.1    Johnson, M.S.2
  • 31
    • 83255194562 scopus 로고    scopus 로고
    • Predicting residue-residue contacts using random forest models
    • 10.1093/bioinformatics/btr579, 22016406
    • Li Y, Fang Y, Fang J. Predicting residue-residue contacts using random forest models. Bioinformatics 2011, 27:3379-3384. 10.1093/bioinformatics/btr579, 22016406.
    • (2011) Bioinformatics , vol.27 , pp. 3379-3384
    • Li, Y.1    Fang, Y.2    Fang, J.3
  • 32
    • 36749031067 scopus 로고    scopus 로고
    • Contact prediction using mutual information and neural nets
    • Shackelford G, Karplus K. Contact prediction using mutual information and neural nets. Proteins 2007, 69(Suppl 8):159-164.
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 159-164
    • Shackelford, G.1    Karplus, K.2
  • 33
    • 34547757477 scopus 로고    scopus 로고
    • Refining intra-protein contact prediction by graph analysis
    • 10.1186/1471-2105-8-S5-S6, 2230507, 18269700
    • Frenkel-Morgenstern M, Magid R, Eyal E, Pietrokovski S. Refining intra-protein contact prediction by graph analysis. BMC Bioinformatics 2007, 8(Suppl 5):S6. 10.1186/1471-2105-8-S5-S6, 2230507, 18269700.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 5
    • Frenkel-Morgenstern, M.1    Magid, R.2    Eyal, E.3    Pietrokovski, S.4
  • 34
    • 34247247779 scopus 로고    scopus 로고
    • Improved residue contact prediction using support vector machines and a large feature set
    • 10.1186/1471-2105-8-113, 1852326, 17407573
    • Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007, 8:113. 10.1186/1471-2105-8-113, 1852326, 17407573.
    • (2007) BMC Bioinformatics , vol.8 , pp. 113
    • Cheng, J.1    Baldi, P.2
  • 35
    • 4043170491 scopus 로고    scopus 로고
    • Protein contact prediction using patterns of correlation
    • 10.1002/prot.20160, 15281121
    • Hamilton N, Burrage K, Ragan MA, Huber T. Protein contact prediction using patterns of correlation. Proteins 2004, 56:679-684. 10.1002/prot.20160, 15281121.
    • (2004) Proteins , vol.56 , pp. 679-684
    • Hamilton, N.1    Burrage, K.2    Ragan, M.A.3    Huber, T.4
  • 36
    • 0035663988 scopus 로고    scopus 로고
    • Prediction of contact maps with neural networks and correlated mutations
    • 10.1093/protein/14.11.835, 11742102
    • Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001, 14:835-843. 10.1093/protein/14.11.835, 11742102.
    • (2001) Protein Eng , vol.14 , pp. 835-843
    • Fariselli, P.1    Olmea, O.2    Valencia, A.3    Casadio, R.4
  • 37
    • 33745610096 scopus 로고    scopus 로고
    • A two-stage approach for improved prediction of residue contact maps
    • 10.1186/1471-2105-7-180, 1484494, 16573808
    • Vullo A, Walsh I, Pollastri G. A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics 2006, 7:180. 10.1186/1471-2105-7-180, 1484494, 16573808.
    • (2006) BMC Bioinformatics , vol.7 , pp. 180
    • Vullo, A.1    Walsh, I.2    Pollastri, G.3
  • 38
    • 0035964191 scopus 로고    scopus 로고
    • TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints
    • 10.1073/pnas.181328398, 56926, 11504922
    • 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 U S A 2001, 98:10125-10130. 10.1073/pnas.181328398, 56926, 11504922.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 10125-10130
    • Kihara, D.1    Lu, H.2    Kolinski, A.3    Skolnick, J.4
  • 39
    • 0033566614 scopus 로고    scopus 로고
    • An empirical energy potential with a reference state for protein fold and sequence recognition
    • 10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829
    • Miyazawa S, Jernigan RL. An empirical energy potential with a reference state for protein fold and sequence recognition. Proteins 1999, 36:357-369. 10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U, 10409829.
    • (1999) Proteins , vol.36 , pp. 357-369
    • Miyazawa, S.1    Jernigan, R.L.2
  • 40
    • 33845377127 scopus 로고
    • Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation
    • Miyazawa S, Jernigan RL. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 41
    • 79955737158 scopus 로고    scopus 로고
    • Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models
    • 10.1002/prot.23015, 3093657, 21560165
    • Gniewek P, Leelananda SP, Kolinski A, Jernigan RL, Kloczkowski A. Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models. Proteins 2011, 79:1923-1929. 10.1002/prot.23015, 3093657, 21560165.
    • (2011) Proteins , vol.79 , pp. 1923-1929
    • Gniewek, P.1    Leelananda, S.P.2    Kolinski, A.3    Jernigan, R.L.4    Kloczkowski, A.5
  • 42
    • 0042889108 scopus 로고    scopus 로고
    • Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
    • 10.1093/bioinformatics/btg186, 12912835
    • Krishnamoorthy B, Tropsha A. Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations. Bioinformatics 2003, 19:1540-1548. 10.1093/bioinformatics/btg186, 12912835.
    • (2003) Bioinformatics , vol.19 , pp. 1540-1548
    • Krishnamoorthy, B.1    Tropsha, A.2
  • 43
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: a protein structure alignment algorithm based on the TM-score
    • 10.1093/nar/gki524, 1084323, 15849316
    • Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005, 33:2302-2309. 10.1093/nar/gki524, 1084323, 15849316.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 44
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • Hildebrand A, Remmert M, Biegert A, Soding J. Fast and accurate automatic structure prediction with HHpred. Proteins 2009, 77(Suppl 9):128-132.
    • (2009) Proteins , vol.77 , Issue.SUPPL. 9 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Soding, J.4
  • 45
    • 77951961719 scopus 로고    scopus 로고
    • How significant is a protein structure similarity with TM-score = 0.5
    • 10.1093/bioinformatics/btq066, 2913670, 20164152
    • Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5. Bioinformatics 2010, 26:889-895. 10.1093/bioinformatics/btq066, 2913670, 20164152.
    • (2010) Bioinformatics , vol.26 , pp. 889-895
    • Xu, J.1    Zhang, Y.2
  • 46
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • 10.1093/nar/gkg571, 168977, 12824330
    • Zemla A. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 2003, 31:3370-3374. 10.1093/nar/gkg571, 168977, 12824330.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 47
    • 79957811210 scopus 로고    scopus 로고
    • CMView: interactive contact map visualization and analysis
    • 10.1093/bioinformatics/btr163, 21471016
    • Vehlow C, Stehr H, Winkelmann M, Duarte JM, Petzold L, Dinse J, Lappe M. CMView: interactive contact map visualization and analysis. Bioinformatics 2011, 27:1573-1574. 10.1093/bioinformatics/btr163, 21471016.
    • (2011) Bioinformatics , vol.27 , pp. 1573-1574
    • Vehlow, C.1    Stehr, H.2    Winkelmann, M.3    Duarte, J.M.4    Petzold, L.5    Dinse, J.6    Lappe, M.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.