메뉴 건너뛰기




Volumn 12, Issue SUPPL. 4, 2011, Pages

Cutoff Scanning Matrix (CSM): Structural classification and function prediction by protein inter-residue distance patterns

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CLASSIFICATION; CONTROLLED STUDY; DATA BASE; ENZYME ACTIVITY; NOISE; PREDICTION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; METABOLISM; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

EID: 84255209052     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S4-S12     Document Type: Article
Times cited : (67)

References (37)
  • 1
    • 75849153303 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt) in 2010
    • 2808944, 19843607, Database issue
    • Consortium TU. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research 2010, 38(Database issue):D142-D148. 2808944, 19843607.
    • (2010) Nucleic Acids Research , vol.38
    • Consortium, T.U.1
  • 3
    • 0028961335 scopus 로고
    • SCOP: a structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 1995, 247(4):536-40.
    • (1995) Journal of Molecular Biology , vol.247 , Issue.4 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 5
    • 22544486576 scopus 로고    scopus 로고
    • Protein function prediction using local 3D templates
    • 10.1016/j.jmb.2005.05.067, 16019027
    • Laskowski RA, Watson JD, Thornton JM. Protein function prediction using local 3D templates. Journal of Molecular Biology 2005, 351(3):614-626. 10.1016/j.jmb.2005.05.067, 16019027.
    • (2005) Journal of Molecular Biology , vol.351 , Issue.3 , pp. 614-626
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 6
    • 22544441094 scopus 로고    scopus 로고
    • ProFunc: a server for predicting protein function from 3D structure
    • 1160175, 15980588, Web Server issue
    • Laskowski RA, Watson JD, Thornton JM. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Research 2005, 33(Web Server issue):W89-93. 1160175, 15980588.
    • (2005) Nucleic Acids Research , vol.33
    • Laskowski, R.A.1    Watson, J.D.2    Thornton, J.M.3
  • 7
    • 20444450051 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structural data
    • 10.1016/j.sbi.2005.04.003, 15963890
    • Watson JD, Roman AL, Thornton JM. Predicting protein function from sequence and structural data. Current Opinion in Structural Biology 2005, 15(3):275-284. 10.1016/j.sbi.2005.04.003, 15963890.
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.3 , pp. 275-284
    • Watson, J.D.1    Roman, A.L.2    Thornton, J.M.3
  • 9
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • 1166865, 3709526
    • Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986, 5(4):823-6. 1166865, 3709526.
    • (1986) EMBO J , vol.5 , Issue.4 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 10
    • 0035014847 scopus 로고    scopus 로고
    • Multi-class protein fold recognition using support vector machines and neural networks
    • 10.1093/bioinformatics/17.4.349, 11301304
    • Ding CH, Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 2001, 17(4):349-58. 10.1093/bioinformatics/17.4.349, 11301304.
    • (2001) Bioinformatics , vol.17 , Issue.4 , pp. 349-358
    • Ding, C.H.1    Dubchak, I.2
  • 11
    • 33747880465 scopus 로고    scopus 로고
    • Ensemble classifier for protein fold pattern recognition
    • 10.1093/bioinformatics/btl170, 16672258
    • Shen HB, Chou KC. Ensemble classifier for protein fold pattern recognition. Bioinformatics 2006, 22(14):1717-22. 10.1093/bioinformatics/btl170, 16672258.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1717-1722
    • Shen, H.B.1    Chou, K.C.2
  • 12
    • 33745616114 scopus 로고    scopus 로고
    • A machine learning information retrieval approach to protein fold recognition
    • 10.1093/bioinformatics/btl102, 16547073
    • Cheng J, Baldi P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics 2006, 22(12):1456-63. 10.1093/bioinformatics/btl102, 16547073.
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1456-1463
    • Cheng, J.1    Baldi, P.2
  • 13
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
    • 10.1093/bioinformatics/btg226, 12967960
    • Barker JA, Thornton JM. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 2003, 19(13):1644-9. 10.1093/bioinformatics/btg226, 12967960.
    • (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 14
    • 34547598665 scopus 로고    scopus 로고
    • PAR-3D: a server to predict protein active site residues
    • 1933233, 17478506, Web Server issue
    • Goyal K, Mohanty D, Mande SC. PAR-3D: a server to predict protein active site residues. Nucleic Acids Research 2007, 35(Web Server issue):W503-5. 1933233, 17478506.
    • (2007) Nucleic Acids Research , vol.35
    • Goyal, K.1    Mohanty, D.2    Mande, S.C.3
  • 15
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • 10.1093/nar/gkg506, 168913, 12824322
    • Stark A, Russell RB. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Research 2003, 31(13):3341-4. 10.1093/nar/gkg506, 168913, 12824322.
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 16
    • 34547573759 scopus 로고    scopus 로고
    • Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces
    • 1933175, 17537808, Web Server issue
    • Shazman S, Celniker G, Haber O, Glaser F, Mandel-Gutfreund Y. Patch Finder Plus (PFplus): a web server for extracting and displaying positive electrostatic patches on protein surfaces. Nucleic Acids Research 2007, 35(Web Server issue):W526-30. 1933175, 17537808.
    • (2007) Nucleic Acids Research , vol.35
    • Shazman, S.1    Celniker, G.2    Haber, O.3    Glaser, F.4    Mandel-Gutfreund, Y.5
  • 17
    • 37349120036 scopus 로고    scopus 로고
    • Prediction of transition metal-binding sites from apo protein structures
    • Babor M, Gerzon S, Raveh B, Sobolev V, Edelman M. Prediction of transition metal-binding sites from apo protein structures. Proteins 2008, 70:208-217.
    • (2008) Proteins , vol.70 , pp. 208-217
    • Babor, M.1    Gerzon, S.2    Raveh, B.3    Sobolev, V.4    Edelman, M.5
  • 18
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • 10.1006/jmbi.1993.1489, 8377180
    • Holm L, Sander C. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology 1993, 233:123-38. 10.1006/jmbi.1993.1489, 8377180.
    • (1993) Journal of Molecular Biology , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 19
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures
    • 10.1016/j.jmb.2004.12.032, 2692023, 15701525
    • Kolodny R, Koehl P, Levitt M. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. Journal of Molecular Biology 2005, 346(4):1173-88. 10.1016/j.jmb.2004.12.032, 2692023, 15701525.
    • (2005) Journal of Molecular Biology , vol.346 , Issue.4 , pp. 1173-1188
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3
  • 20
    • 9644283060 scopus 로고    scopus 로고
    • Predicting enzyme class from protein structure without alignments
    • 10.1016/j.jmb.2004.10.024, 15567421
    • Dobson PD, Doig AJ. Predicting enzyme class from protein structure without alignments. Journal of Molecular Biology 2005, 345:187-199. 10.1016/j.jmb.2004.10.024, 15567421.
    • (2005) Journal of Molecular Biology , vol.345 , pp. 187-199
    • Dobson, P.D.1    Doig, A.J.2
  • 22
    • 55449125498 scopus 로고    scopus 로고
    • The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
    • 10.1371/journal.pcbi.1000160, 2518264, 18974821
    • Punta M, Ofran Y. The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Computational Biology 2008, 4(10):e1000160. 10.1371/journal.pcbi.1000160, 2518264, 18974821.
    • (2008) PLoS Computational Biology , vol.4 , Issue.10
    • Punta, M.1    Ofran, Y.2
  • 24
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • 10.1038/nrm2281, 18037900
    • Lee D, Redfen O, C O. Predicting protein function from sequence and structure. Nature Reviews: Molecular Cell Biology 2007, 8(12):995-1005. 10.1038/nrm2281, 18037900.
    • (2007) Nature Reviews: Molecular Cell Biology , vol.8 , Issue.12 , pp. 995-1005
    • Lee, D.1    Redfen, O.2    C, O.3
  • 25
    • 77949609215 scopus 로고    scopus 로고
    • Atomic interaction networks in the core of protein domains and their native folds
    • 10.1371/journal.pone.0009391, 2826414, 20186337
    • Soundararajan V, Raman R, Raguram S, Sasisekharan V, Sasisekharan R. Atomic interaction networks in the core of protein domains and their native folds. PLoS One 2010, 5(2):e9391. 10.1371/journal.pone.0009391, 2826414, 20186337.
    • (2010) PLoS One , vol.5 , Issue.2
    • Soundararajan, V.1    Raman, R.2    Raguram, S.3    Sasisekharan, V.4    Sasisekharan, R.5
  • 27
    • 0001571646 scopus 로고
    • Sur la sphere vide. A la memoire de Georges Voronoi
    • Delaunay B. Sur la sphere vide. A la memoire de Georges Voronoi. Izv Akad Nauk SSSR 1934, 7:793-800.
    • (1934) Izv Akad Nauk SSSR , vol.7 , pp. 793-800
    • Delaunay, B.1
  • 28
    • 33745027619 scopus 로고    scopus 로고
    • A gold standard set of mechanistically diverse enzyme superfamilies
    • 10.1186/gb-2006-7-1-r8, 1431709, 16507141
    • Brown SD, Gerlt JA, Seffernick JL, Babbitt PC. A gold standard set of mechanistically diverse enzyme superfamilies. Genome Biology 2006, 7:R8. 10.1186/gb-2006-7-1-r8, 1431709, 16507141.
    • (2006) Genome Biology , vol.7
    • Brown, S.D.1    Gerlt, J.A.2    Seffernick, J.L.3    Babbitt, P.C.4
  • 29
    • 77954053524 scopus 로고    scopus 로고
    • Automatic structure classification of small proteins using random forest
    • 2837025, 20043860
    • Jain P, Hirst JD. Automatic structure classification of small proteins using random forest. BMC Bioinformatics 2010, 11(364):1-14. 2837025, 20043860.
    • (2010) BMC Bioinformatics , vol.11 , Issue.364 , pp. 1-14
    • Jain, P.1    Hirst, J.D.2
  • 30
    • 0030777303 scopus 로고    scopus 로고
    • CATH - a hierarchic classification of protein domain structures
    • 10.1016/S0969-2126(97)00260-8, 9309224
    • Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-108. 10.1016/S0969-2126(97)00260-8, 9309224.
    • (1997) Structure , vol.5 , Issue.8 , pp. 1093-1108
    • Orengo, C.A.1    Michie, A.D.2    Jones, S.3    Jones, D.T.4    Swindells, M.B.5    Thornton, J.M.6
  • 31
    • 33750605056 scopus 로고    scopus 로고
    • Matrix Methods in Data Mining and Pattern Recognition (Fundamentals of Algorithms)
    • Eldén L. Matrix Methods in Data Mining and Pattern Recognition (Fundamentals of Algorithms). Society for Industrial and Applied Mathematics 2007,
    • (2007) Society for Industrial and Applied Mathematics
    • Eldén, L.1
  • 32
    • 33646719673 scopus 로고    scopus 로고
    • Numerical linear algebra in data mining
    • Eldén L. Numerical linear algebra in data mining. Acta Numerica 2006, 15:327-384.
    • (2006) Acta Numerica , vol.15 , pp. 327-384
    • Eldén, L.1
  • 33
    • 0029546874 scopus 로고
    • Using linear algebra for intelligent information retrieval
    • Berry MW, Dumais ST, O'Brien GW. Using linear algebra for intelligent information retrieval. SIAM review 1995, 37(4):573-595.
    • (1995) SIAM review , vol.37 , Issue.4 , pp. 573-595
    • Berry, M.W.1    Dumais, S.T.2    O'Brien, G.W.3
  • 36
    • 0003957032 scopus 로고    scopus 로고
    • Data Mining: Practical Machine Learning Tools and Techniques
    • Morgan Kaufmann, second
    • Witten IH, Frank E. Data Mining: Practical Machine Learning Tools and Techniques. 2005, Morgan Kaufmann, second.
    • (2005)
    • Witten, I.H.1    Frank, E.2
  • 37
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for sequence and structure analysis
    • 10.1093/nar/28.1.254, 102434, 10592239
    • Brenner SE, Koehl P, Levitt M. The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Research 2000, 28:254-256. 10.1093/nar/28.1.254, 102434, 10592239.
    • (2000) Nucleic Acids Research , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.