메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

ClusCo: Clustering and comparison of protein models

Author keywords

[No Author keywords available]

Indexed keywords

CALCULATING SIMILARITIES; COMPUTATION PROGRAM; CONTACT MAP OVERLAP; K-MEANS CLUSTERING; NATIVE STRUCTURES; PARALLEL EXECUTIONS; SIMILARITY MEASURE; STRUCTURAL COMPARISON;

EID: 84874058893     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-62     Document Type: Article
Times cited : (31)

References (24)
  • 1
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr 1976, 32:922-923.
    • (1976) Acta Crystallogr , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 2
    • 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(13):3370-3374. 10.1093/nar/gkg571, 168977, 12824330.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3370-3374
    • Zemla, A.1
  • 3
    • 0033670439 scopus 로고    scopus 로고
    • MaxSub: an automated measure for the assessment of protein structure prediction quality
    • 10.1093/bioinformatics/16.9.776, 11108700
    • Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000, 16(9):776-785. 10.1093/bioinformatics/16.9.776, 11108700.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 776-785
    • Siew, N.1    Elofsson, A.2    Rychlewski, L.3    Fischer, D.4
  • 4
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • 10.1002/prot.20264, 15476259
    • Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57(4):702-710. 10.1002/prot.20264, 15476259.
    • (2004) Proteins , vol.57 , Issue.4 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 5
    • 84986435778 scopus 로고
    • Algorithms for clustering molecular dynamics configurations
    • Torda AE, van Gunsteren WF. Algorithms for clustering molecular dynamics configurations. J Comput Chem 1994, 15(12):1331-1340.
    • (1994) J Comput Chem , vol.15 , Issue.12 , pp. 1331-1340
    • Torda, A.E.1    van Gunsteren, W.F.2
  • 6
    • 0032530578 scopus 로고    scopus 로고
    • Clustering of low-energy conformations near the native structures of small proteins
    • Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. P Natl Acad Sci USA 1998, 95(19):11158-11162.
    • (1998) P Natl Acad Sci USA , vol.95 , Issue.19 , pp. 11158-11162
    • Shortle, D.1    Simons, K.T.2    Baker, D.3
  • 7
    • 3242779291 scopus 로고    scopus 로고
    • Protein modeling and structure prediction with a reduced representation
    • Kolinski A. Protein modeling and structure prediction with a reduced representation. Acta Biochim Pol 2004, 51(2):349-371.
    • (2004) Acta Biochim Pol , vol.51 , Issue.2 , pp. 349-371
    • Kolinski, A.1
  • 8
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: a unified platform for automated protein structure and function prediction
    • 10.1038/nprot.2010.5, 2849174, 20360767
    • Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010, 5(4):725-738. 10.1038/nprot.2010.5, 2849174, 20360767.
    • (2010) Nat Protoc , vol.5 , Issue.4 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 9
    • 84862225232 scopus 로고    scopus 로고
    • Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
    • Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 2012, 80(7):1715-1735.
    • (2012) Proteins , vol.80 , Issue.7 , pp. 1715-1735
    • Xu, D.1    Zhang, Y.2
  • 11
    • 0001457509 scopus 로고
    • Some methods for classification and analysis of multiVariate observations
    • Berkeley: University of California Press, Cam LML, Neyman J.
    • MacQueen JB. Some methods for classification and analysis of multiVariate observations. Proc. of the fifth Berkeley Symposium on Mathematical Statistics and Probability, Volume 1 1967, 281-297. Berkeley: University of California Press, Cam LML, Neyman J..
    • (1967) Proc. of the fifth Berkeley Symposium on Mathematical Statistics and Probability, Volume 1 , pp. 281-297
    • MacQueen, J.B.1
  • 12
    • 3142756502 scopus 로고    scopus 로고
    • Open source clustering software
    • 10.1093/bioinformatics/bth078, 14871861
    • de Hoon MJL, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004, 20(9):1453-1454. 10.1093/bioinformatics/bth078, 14871861.
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1453-1454
    • de Hoon, M.J.L.1    Imoto, S.2    Nolan, J.3    Miyano, S.4
  • 13
    • 0037230925 scopus 로고    scopus 로고
    • Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation
    • Brüschweiler R. Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation. Proteins 2003, 50:26-34.
    • (2003) Proteins , vol.50 , pp. 26-34
    • Brüschweiler, R.1
  • 14
    • 79955871892 scopus 로고    scopus 로고
    • Finding nearly optimal GDT scores
    • 10.1089/cmb.2010.0123, 3607910, 21554017
    • Li SC, Bu D, Xu J, Li M. Finding nearly optimal GDT scores. J Comput Biol 2011, 18(5):693-704. 10.1089/cmb.2010.0123, 3607910, 21554017.
    • (2011) J Comput Biol , vol.18 , Issue.5 , pp. 693-704
    • Li, S.C.1    Bu, D.2    Xu, J.3    Li, M.4
  • 16
    • 84861473258 scopus 로고    scopus 로고
    • Fast structure similarity searches among protein models: efficient clustering of protein fragments
    • 10.1186/1748-7188-7-16, 3403935, 22642815
    • Fogolari F, Corazza A, Viglino P, Esposito G. Fast structure similarity searches among protein models: efficient clustering of protein fragments. Algorithms Mol Biol 2012, 7:16. 10.1186/1748-7188-7-16, 3403935, 22642815.
    • (2012) Algorithms Mol Biol , vol.7 , pp. 16
    • Fogolari, F.1    Corazza, A.2    Viglino, P.3    Esposito, G.4
  • 17
    • 0033853177 scopus 로고    scopus 로고
    • Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction
    • 10.1110/ps.9.7.1399, 2144680, 10933507
    • Samudrala R, Levitt M. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 2000, 9(7):1399-1401. 10.1110/ps.9.7.1399, 2144680, 10933507.
    • (2000) Protein Sci , vol.9 , Issue.7 , pp. 1399-1401
    • Samudrala, R.1    Levitt, M.2
  • 18
    • 29244479220 scopus 로고    scopus 로고
    • A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators
    • 10.1186/1471-2105-6-301, 1351271, 16354298
    • Fogolari F, Tosatto SCE, Colombo G. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators. BMC Bioinformatics 2005, 6:301. 10.1186/1471-2105-6-301, 1351271, 16354298.
    • (2005) BMC Bioinformatics , vol.6 , pp. 301
    • Fogolari, F.1    Tosatto, S.C.E.2    Colombo, G.3
  • 19
    • 84855684085 scopus 로고    scopus 로고
    • Durandal: fast exact clustering of protein decoys
    • 10.1002/jcc.21988, 22120171
    • Berenger F, Shrestha R, Zhou Y, Simoncini D, Zhang KYJ. Durandal: fast exact clustering of protein decoys. J Comput Chem 2012, 33(4):471-474. 10.1002/jcc.21988, 22120171.
    • (2012) J Comput Chem , vol.33 , Issue.4 , pp. 471-474
    • Berenger, F.1    Shrestha, R.2    Zhou, Y.3    Simoncini, D.4    Zhang, K.Y.J.5
  • 20
    • 77949527229 scopus 로고    scopus 로고
    • Calibur: a tool for clustering large numbers of protein decoys
    • 10.1186/1471-2105-11-25, 2881085, 20070892
    • Li SC, Ng YK. Calibur: a tool for clustering large numbers of protein decoys. BMC Bioinformatics 2010, 11:25. 10.1186/1471-2105-11-25, 2881085, 20070892.
    • (2010) BMC Bioinformatics , vol.11 , pp. 25
    • Li, S.C.1    Ng, Y.K.2
  • 21
    • 1942519275 scopus 로고    scopus 로고
    • SPICKER: a clustering approach to identify near-native protein folds
    • 10.1002/jcc.20011, 15011258
    • Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004, 25(6):865-871. 10.1002/jcc.20011, 15011258.
    • (2004) J Comput Chem , vol.25 , Issue.6 , pp. 865-871
    • Zhang, Y.1    Skolnick, J.2
  • 22
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • 10.1186/1741-7007-5-17, 1878469, 17488521
    • Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007, 5:17. 10.1186/1741-7007-5-17, 1878469, 17488521.
    • (2007) BMC Biol , vol.5 , pp. 17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 23
    • 29844457403 scopus 로고    scopus 로고
    • Rapid calculation of RMSDs using a quaternion-based characteristic polynomial
    • Theobald DL. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallogr A 2005, 61(Pt 4):478-80.
    • (2005) Acta Crystallogr A , vol.61 , Issue.PART 4 , pp. 478-480
    • Theobald, D.L.1
  • 24
    • 84865079620 scopus 로고    scopus 로고
    • Accelerated protein structure comparison using TM-score-GPU
    • 10.1093/bioinformatics/bts345, 3413391, 22718788
    • Hung LH, Samudrala R. Accelerated protein structure comparison using TM-score-GPU. Bioinformatics 2012, 28(16):2191-2192. 10.1093/bioinformatics/bts345, 3413391, 22718788.
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2191-2192
    • Hung, L.H.1    Samudrala, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.