메뉴 건너뛰기




Volumn 328, Issue , 2013, Pages 77-88

The utility of artificially evolved sequences in protein threading and fold recognition

Author keywords

Artificial sequences; Evolved sequences; Protein structure modeling; Protein threading; Template based modeling

Indexed keywords

PROTEIN;

EID: 84877070744     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2013.03.018     Document Type: Article
Times cited : (8)

References (60)
  • 2
    • 0002651837 scopus 로고
    • An overview of evolutionary algorithms for parameter optimization
    • Back T., Schwefel H.P. An overview of evolutionary algorithms for parameter optimization. Evol. Comput. 1993, 1:1-23.
    • (1993) Evol. Comput. , vol.1 , pp. 1-23
    • Back, T.1    Schwefel, H.P.2
  • 3
    • 27144459217 scopus 로고
    • In: Proceedings of the Fourth International Conference on Genetic Algorithms, San Mateo, CA
    • Back, T., Hoffmeister, F., Schwefel, H.P., 1992. A Survey of Evolution Strategies. In: Proceedings of the Fourth International Conference on Genetic Algorithms, San Mateo, CA, pp. 2-9.
    • (1992) A Survey of Evolution Strategies. , pp. 2-9
    • Back, T.1    Hoffmeister, F.2    Schwefel, H.P.3
  • 5
    • 62649147821 scopus 로고    scopus 로고
    • Sequence context-specific profiles for homology searching
    • Biegert A., Soding J. Sequence context-specific profiles for homology searching. Proc. Natl. Acad. Sci. USA 2009, 106:3770-3775. 10.1073/pnas.0810767106.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 3770-3775
    • Biegert, A.1    Soding, J.2
  • 7
    • 38349100452 scopus 로고    scopus 로고
    • A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
    • Brylinski M., Skolnick J. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation. Proc. Natl. Acad. Sci. USA 2008, 105:129-134.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 129-134
    • Brylinski, M.1    Skolnick, J.2
  • 8
    • 79551476059 scopus 로고    scopus 로고
    • FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level
    • [doi]
    • Brylinski M., Skolnick J. FINDSITE-metal: integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level. Proteins 2011, 79:735-751. [doi]. 10.1002/prot.22913.
    • (2011) Proteins , vol.79 , pp. 735-751
    • Brylinski, M.1    Skolnick, J.2
  • 10
    • 78649797219 scopus 로고    scopus 로고
    • Effect of using suboptimal alignments in template-based protein structure prediction
    • Chen H., Kihara D. Effect of using suboptimal alignments in template-based protein structure prediction. Proteins 2011, 79:315-334. 10.1002/prot.22885.
    • (2011) Proteins , vol.79 , pp. 315-334
    • Chen, H.1    Kihara, D.2
  • 11
    • 79953873680 scopus 로고    scopus 로고
    • Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations
    • Dai L., Zhou Y. Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. J. Mol. Biol. 2011, 408:585-595. 10.1016/j.jmb.2011.02.056.
    • (2011) J. Mol. Biol. , vol.408 , pp. 585-595
    • Dai, L.1    Zhou, Y.2
  • 12
    • 0027983037 scopus 로고
    • Convergent evolution: the need to be explicit
    • Doolittle R.F. Convergent evolution: the need to be explicit. Trends Biochem. Sci. 1994, 19:15-18.
    • (1994) Trends Biochem. Sci. , vol.19 , pp. 15-18
    • Doolittle, R.F.1
  • 14
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 15
    • 0035965145 scopus 로고    scopus 로고
    • Prediction of functionally important residues based solely on the computed energetics of protein structure
    • Elcock A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 2001, 312:885-896. 10.1006/jmbi.2001.5009.
    • (2001) J. Mol. Biol. , vol.312 , pp. 885-896
    • Elcock, A.H.1
  • 16
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • Frishman D., Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995, 23:566-579. 10.1002/prot.340230412.
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 17
    • 33646002994 scopus 로고    scopus 로고
    • Comparative modeling for protein structure prediction
    • Ginalski K. Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol. 2006, 16:172-177. 10.1016/j.sbi.2006.02.003.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 172-177
    • Ginalski, K.1
  • 19
    • 27344440132 scopus 로고    scopus 로고
    • Conservation and relative importance of residues across protein-protein interfaces
    • Guharoy M., Chakrabarti P. Conservation and relative importance of residues across protein-protein interfaces. Proc. Natl. Acad. Sci. USA 2005, 102:15447-15452. 10.1073/pnas.0505425102.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15447-15452
    • Guharoy, M.1    Chakrabarti, P.2
  • 20
    • 0030735959 scopus 로고    scopus 로고
    • An introduction to multisensor data fusion
    • Hall D.L., Llinas J. An introduction to multisensor data fusion. Proc. IEEE 1997, 85:6-23.
    • (1997) Proc. IEEE , vol.85 , pp. 6-23
    • Hall, D.L.1    Llinas, J.2
  • 21
  • 22
    • 32344440995 scopus 로고    scopus 로고
    • Blind docking of drug-sized compounds to proteins with up to a thousand residues
    • Hetenyi C., van der Spoel D. Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett. 2006, 580:1447-1450. 10.1016/j.febslet.2006.01.074.
    • (2006) FEBS Lett. , vol.580 , pp. 1447-1450
    • Hetenyi, C.1    van der Spoel, D.2
  • 23
    • 33750029942 scopus 로고    scopus 로고
    • LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation
    • Huang B., Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 2006, 6:19. 10.1186/1472-6807-6-19.
    • (2006) BMC Struct. Biol. , vol.6 , pp. 19
    • Huang, B.1    Schroeder, M.2
  • 24
    • 0029887381 scopus 로고    scopus 로고
    • Hidden Markov models for sequence analysis: extension and analysis of the basic method
    • Hughey R., Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput. Appl. Biosci. 1996, 12:95-107.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 95-107
    • Hughey, R.1    Krogh, A.2
  • 25
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 1999, 292:195-202. 10.1006/jmbi.1999.3091.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 26
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones D.T., Taylor W.R., Thornton J.M. A new approach to protein fold recognition. Nature 1992, 358:86-89. 10.1038/358086a0.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 27
    • 2442436935 scopus 로고    scopus 로고
    • Evaluation of local structure alphabets based on residue burial
    • Karchin R., Cline M., Karplus K. Evaluation of local structure alphabets based on residue burial. Proteins 2004, 55:508-518. 10.1002/prot.20008.
    • (2004) Proteins , vol.55 , pp. 508-518
    • Karchin, R.1    Cline, M.2    Karplus, K.3
  • 28
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • Kitano H. Systems biology: a brief overview. Science 2002, 295:1662-1664. 10.1126/science.1069492.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 29
    • 30344475200 scopus 로고    scopus 로고
    • Progress over the first decade of CASP experiments
    • Kryshtafovych A., Venclovas C., Fidelis K., Molt J. Progress over the first decade of CASP experiments. Proteins 2005, 61(7):225-236. 10.1002/prot.20740.
    • (2005) Proteins , vol.61 , Issue.7 , pp. 225-236
    • Kryshtafovych, A.1    Venclovas, C.2    Fidelis, K.3    Molt, J.4
  • 30
    • 0043123216 scopus 로고    scopus 로고
    • GeneSilico protein structure prediction meta-server
    • Kurowski M.A., Bujnicki J.M. GeneSilico protein structure prediction meta-server. Nucl. Acids Res. 2003, 31:3305-3307.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3305-3307
    • Kurowski, M.A.1    Bujnicki, J.M.2
  • 31
    • 80055097657 scopus 로고    scopus 로고
    • Using structure to explore the sequence alignment space of remote homologs
    • Kuziemko A., Honig B., Petrey D. Using structure to explore the sequence alignment space of remote homologs. PLoS Comput. Biol. 2011, 7:e1002175. 10.1371/journal.pcbi.1002175.
    • (2011) PLoS Comput. Biol. , vol.7
    • Kuziemko, A.1    Honig, B.2    Petrey, D.3
  • 32
    • 79960036791 scopus 로고    scopus 로고
    • DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
    • Liu S., Vakser I.A. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. BMC Bioinform. 2011, 12:280. 10.1186/1471-2105-12-280.
    • (2011) BMC Bioinform. , vol.12 , pp. 280
    • Liu, S.1    Vakser, I.A.2
  • 33
    • 0034780030 scopus 로고    scopus 로고
    • Pcons: a neural-network-based consensus predictor that improves fold recognition
    • Lundstrom J., Rychlewski L., Bujnicki J., Elofsson A. Pcons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci. 2001, 10:2354-2362.
    • (2001) Protein Sci. , vol.10 , pp. 2354-2362
    • Lundstrom, J.1    Rychlewski, L.2    Bujnicki, J.3    Elofsson, A.4
  • 35
    • 33746358516 scopus 로고    scopus 로고
    • High throughput profile-profile based fold recognition for the entire human proteome
    • McGuffin L.J., Smith R.T., Bryson K., Sorensen S.A., Jones D.T. High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinform. 2006, 7:288. 10.1186/1471-2105-7-288.
    • (2006) BMC Bioinform. , vol.7 , pp. 288
    • McGuffin, L.J.1    Smith, R.T.2    Bryson, K.3    Sorensen, S.A.4    Jones, D.T.5
  • 37
    • 80054685109 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP)-round IX
    • Moult J., Fidelis K., Kryshtafovych A., Tramontano A. Critical assessment of methods of protein structure prediction (CASP)-round IX. Proteins 2011, 79(10):1-5. 10.1002/prot.23200.
    • (2011) Proteins , vol.79 , Issue.10 , pp. 1-5
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Tramontano, A.4
  • 38
    • 74249119329 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction-Round VIII
    • Moult J., Fidelis K., Kryshtafovych A., Rost B., Tramontano A. Critical assessment of methods of protein structure prediction-Round VIII. Proteins 2009, 77(9):1-4. 10.1002/prot.22589.
    • (2009) Proteins , vol.77 , Issue.9 , pp. 1-4
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Rost, B.4    Tramontano, A.5
  • 40
    • 58649097284 scopus 로고    scopus 로고
    • Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
    • Pandit S.B., Skolnick J. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinform. 2008, 9:531. 10.1186/1471-2105-9-531.
    • (2008) BMC Bioinform. , vol.9 , pp. 531
    • Pandit, S.B.1    Skolnick, J.2
  • 41
    • 77957934494 scopus 로고    scopus 로고
    • TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates
    • Pandit S.B., Skolnick J. TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates. Proteins 2010, 78:2769-2780. 10.1002/prot.22791.
    • (2010) Proteins , vol.78 , pp. 2769-2780
    • Pandit, S.B.1    Skolnick, J.2
  • 42
    • 77954196482 scopus 로고    scopus 로고
    • Low-homology protein threading
    • Peng J., Xu J. Low-homology protein threading. Bioinformatics 2010, 26:i294-i300. 10.1093/bioinformatics/btq192.
    • (2010) Bioinformatics , vol.26
    • Peng, J.1    Xu, J.2
  • 43
    • 79955715769 scopus 로고    scopus 로고
    • A multiple-template approach to protein threading
    • Peng J., Xu J. A multiple-template approach to protein threading. Proteins 2011, 79:1930-1939. 10.1002/prot.23016.
    • (2011) Proteins , vol.79 , pp. 1930-1939
    • Peng, J.1    Xu, J.2
  • 44
    • 0030627901 scopus 로고    scopus 로고
    • Protein structures sustain evolutionary drift
    • Rost B. Protein structures sustain evolutionary drift. Fold Des. 1997, 2:S19-S24.
    • (1997) Fold Des. , vol.2
    • Rost, B.1
  • 45
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999, 12:85-94.
    • (1999) Protein Eng. , vol.12 , pp. 85-94
    • Rost, B.1
  • 46
    • 0037423702 scopus 로고    scopus 로고
    • COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
    • Sadreyev R., Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. J. Mol. Biol. 2003, 326:317-336.
    • (2003) J. Mol. Biol. , vol.326 , pp. 317-336
    • Sadreyev, R.1    Grishin, N.2
  • 47
    • 0042685140 scopus 로고    scopus 로고
    • A proposed measure for psi-induced bunching of randomly spaced events
    • Schmidt H. A proposed measure for psi-induced bunching of randomly spaced events. J. Parapsychol. 2000, 64:301-316.
    • (2000) J. Parapsychol. , vol.64 , pp. 301-316
    • Schmidt, H.1
  • 49
    • 67449108422 scopus 로고    scopus 로고
    • FINDSITE: a combined evolution/structure-based approach to protein function prediction
    • doi:bbp017 [pii]10.1093/bib/bbp017 [doi]
    • Skolnick J., Brylinski M. FINDSITE: a combined evolution/structure-based approach to protein function prediction. Brief Bioinform. 2009, 10:378-391. doi:bbp017 [pii]10.1093/bib/bbp017 [doi].
    • (2009) Brief Bioinform. , vol.10 , pp. 378-391
    • Skolnick, J.1    Brylinski, M.2
  • 50
    • 84862276163 scopus 로고    scopus 로고
    • Further evidence for the likely completeness of the library of solved single domain protein structures
    • Skolnick J., Zhou H., Brylinski M. Further evidence for the likely completeness of the library of solved single domain protein structures. J. Phys. Chem. B 2012, 116:6654-6664. 10.1021/jp211052j.
    • (2012) J. Phys. Chem. B , vol.116 , pp. 6654-6664
    • Skolnick, J.1    Zhou, H.2    Brylinski, M.3
  • 51
    • 70349461173 scopus 로고    scopus 로고
    • The continuity of protein structure space is an intrinsic property of proteins
    • Skolnick J., Arakaki A.K., Lee S.Y., Brylinski M. The continuity of protein structure space is an intrinsic property of proteins. Proc. Natl. Acad. Sci. USA 2009, 106:15690-15695. 10.1073/pnas.0907683106.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 15690-15695
    • Skolnick, J.1    Arakaki, A.K.2    Lee, S.Y.3    Brylinski, M.4
  • 52
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960. 10.1093/bioinformatics/bti125.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 54
    • 77954299402 scopus 로고    scopus 로고
    • 3DLigandSite: predicting ligand-binding sites using similar structures
    • Wass M.N., Kelley L.A., Sternberg M.J. 3DLigandSite: predicting ligand-binding sites using similar structures. Nucleic Acids Res 2010, 38:W469-W473. 10.1093/nar/gkq406.
    • (2010) Nucleic Acids Res , vol.38
    • Wass, M.N.1    Kelley, L.A.2    Sternberg, M.J.3
  • 55
    • 34250851687 scopus 로고    scopus 로고
    • LOMETS: a local meta-threading-server for protein structure prediction
    • Wu S., Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res. 2007, 35:3375-3382. 10.1093/nar/gkm251.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 3375-3382
    • Wu, S.1    Zhang, Y.2
  • 56
    • 1642534609 scopus 로고    scopus 로고
    • An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state
    • Zhang C., Liu S., Zhou H., Zhou Y. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci. 2004, 13:400-411. 10.1110/ps.03348304.
    • (2004) Protein Sci. , vol.13 , pp. 400-411
    • Zhang, C.1    Liu, S.2    Zhou, H.3    Zhou, Y.4
  • 57
    • 74249106219 scopus 로고    scopus 로고
    • I-TASSER: fully automated protein structure prediction in CASP8
    • Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009, 77(9):100-113. 10.1002/prot.22588.
    • (2009) Proteins , vol.77 , Issue.9 , pp. 100-113
    • Zhang, Y.1
  • 58
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang Y., Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57:702-710. 10.1002/prot.20264.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 59
    • 12844288890 scopus 로고    scopus 로고
    • The protein structure prediction problem could be solved using the current PDB library
    • Zhang Y., Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc. Natl. Acad. Sci. USA 2005, 102:1029-1034. 10.1073/pnas.0407152101.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 1029-1034
    • Zhang, Y.1    Skolnick, J.2
  • 60
    • 33644553089 scopus 로고    scopus 로고
    • On the origin and highly likely completeness of single-domain protein structures
    • Zhang Y., Hubner I.A., Arakaki A.K., Shakhnovich E., Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proc. Natl. Acad. Sci. USA 2006, 103:2605-2610. 10.1073/pnas.0509379103.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 2605-2610
    • Zhang, Y.1    Hubner, I.A.2    Arakaki, A.K.3    Shakhnovich, E.4    Skolnick, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.