메뉴 건너뛰기




Volumn 6, Issue , 2006, Pages

Secondary structure spatial conformation footprint: A novel method for fast protein structure comparison and classification

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE;

EID: 33747079562     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-12     Document Type: Article
Times cited : (28)

References (28)
  • 1
    • 12344271154 scopus 로고    scopus 로고
    • Survey of current protein family databases and their application in comparative, structural and functional genomics
    • Redfern O, Alastair G, Maibaum M, Orengo C: Survey of current protein family databases and their application in comparative, structural and functional genomics. J Chromatogr B Analyt Technol Biomed Life Sci 2005, 815:97-107.
    • (2005) J Chromatogr B Analyt Technol Biomed Life Sci , vol.815 , pp. 97-107
    • Redfern, O.1    Alastair, G.2    Maibaum, M.3    Orengo, C.4
  • 2
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A, Brenner S, Hubbard T, Chotia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.2    Hubbard, T.3    Chotia, C.4
  • 5
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov R, Wolfson H: Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci USA 1991, 88:10495-10499.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.2
  • 6
    • 0026759751 scopus 로고
    • Fast structure alignment for protein databank searching
    • Orengo C, Brown N, Taylor W: Fast structure alignment for protein databank searching. Proteins 1992, 14:139-167.
    • (1992) Proteins , vol.14 , pp. 139-167
    • Orengo, C.1    Brown, N.2    Taylor, W.3
  • 7
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L, Sander C: Protein structure comparison by alignment of distance matrices. J Mol Biol 1993, 233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 8
    • 0029936121 scopus 로고    scopus 로고
    • Surprising similarities in structure comparison
    • Gibrat J, Madej T, Bryant S: Surprising similarities in structure comparison. Curr Opin Struct Biol 1996, 6:377-385.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 377-385
    • Gibrat, J.1    Madej, T.2    Bryant, S.3
  • 9
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins
    • Gerstein M, Levitt M: Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Science 1998, 7:445-456.
    • (1998) Protein Science , vol.7 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 10
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov I, Bourne P: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering 1998, 11:739-747.
    • (1998) Protein Engineering , vol.11 , pp. 739-747
    • Shindyalov, I.1    Bourne, P.2
  • 11
    • 0029174540 scopus 로고
    • 3-D Lookup: Fast protein structure database searches at 90% reliability
    • Holm L, Sander C: 3-D Lookup: fast protein structure database searches at 90% reliability. Proc Int Conf Intell Syst Mol Biol 1995, 3:179-87.
    • (1995) Proc Int Conf Intell Syst Mol Biol , vol.3 , pp. 179-187
    • Holm, L.1    Sander, C.2
  • 13
    • 0034458972 scopus 로고    scopus 로고
    • The ups and downs of protein topology; rapid comparison of protein structure
    • Martin A: The ups and downs of protein topology; rapid comparison of protein structure. Protein Engineering 2000, 13:829-837.
    • (2000) Protein Engineering , vol.13 , pp. 829-837
    • Martin, A.1
  • 14
    • 0037422619 scopus 로고    scopus 로고
    • Automatic classification of protein structure by using Gauss integrals
    • Rogen P, Fain B: Automatic classification of protein structure by using Gauss integrals. Proc Natl Acad Sci USA 2003, 100:119-124.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 119-124
    • Rogen, P.1    Fain, B.2
  • 15
    • 1842781469 scopus 로고    scopus 로고
    • Protein structure comparison in 3D based on secondary structure matching (SSM) followed by CA alignment, scored by a new structural similarity function
    • Krissinel E, Henrick K: Protein structure comparison in 3D based on secondary structure matching (SSM) followed by CA alignment, scored by a new structural similarity function. Proceedings of the 5th International Conference on Molecular Structural Biology 2003.
    • (2003) Proceedings of the 5th International Conference on Molecular Structural Biology
    • Krissinel, E.1    Henrick, K.2
  • 16
    • 2442694738 scopus 로고    scopus 로고
    • PSI: Indexing protein structures for fast similarity search
    • Camoglu O, Kahveci T, Singh A: PSI: indexing protein structures for fast similarity search. Bioinformatics 2003:i81-i83.
    • (2003) Bioinformatics
    • Camoglu, O.1    Kahveci, T.2    Singh, A.3
  • 17
    • 1642389927 scopus 로고    scopus 로고
    • Local feature frequency profile: A method to measure structural similarity in proteins
    • Choi I, Kwon J, Kim S: Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci USA 2004, 101:3797-3802.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3797-3802
    • Choi, I.1    Kwon, J.2    Kim, S.3
  • 18
    • 12844261137 scopus 로고    scopus 로고
    • PROuST: A comparison method of three-dimensional structures of proteins using indexing techniques
    • Comin M, Guerra C, Zanotti G: PROuST: A comparison method of three-dimensional structures of proteins using indexing techniques. J Comput Biol 2004, 11:1061-1072.
    • (2004) J Comput Biol , vol.11 , pp. 1061-1072
    • Comin, M.1    Guerra, C.2    Zanotti, G.3
  • 19
    • 0036304230 scopus 로고    scopus 로고
    • Protein fold similarity estimated by a probabilistic approach based on C[alpha]-C[alpha] distance comparison
    • Carugo O, Pongor S: Protein fold similarity estimated by a probabilistic approach based on C[alpha]-C[alpha] distance comparison. J Mol Biol 2002, 315:887-898.
    • (2002) J Mol Biol , vol.315 , pp. 887-898
    • Carugo, O.1    Pongor, S.2
  • 20
    • 25144432432 scopus 로고    scopus 로고
    • Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm
    • Gáspári Z, Vlahovicek K, Pongor S: Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm. Bioinformatics 2005, 21(15):3322-3323.
    • (2005) Bioinformatics , vol.21 , Issue.15 , pp. 3322-3323
    • Gáspári, Z.1    Vlahovicek, K.2    Pongor, S.3
  • 21
    • 33645678626 scopus 로고    scopus 로고
    • Fold classification based on secondary structure-how much is gained by including loop topology?
    • Jeong J, Berman P, Przytycka T: Fold classification based on secondary structure-how much is gained by including loop topology? BMC Struct Biol 2006, 6:3.
    • (2006) BMC Struct Biol , vol.6 , pp. 3
    • Jeong, J.1    Berman, P.2    Przytycka, T.3
  • 24
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, Sander C: Mapping the protein universe. Science 1996, 273(5275):595-603.
    • (1996) Science , vol.273 , Issue.5275 , pp. 595-603
    • Holm, L.1    Sander, C.2
  • 25
    • 84872265900 scopus 로고    scopus 로고
    • The MMDB Database [http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml]
    • The MMDB Database
  • 26
    • 0020997912 scopus 로고
    • Secondary structure definition by the program DSSP
    • Kabsch W, Sander C: Secondary structure definition by the program DSSP. Biopolymers 1983, 22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 28
    • 84872270870 scopus 로고    scopus 로고
    • The BioPython Project
    • The BioPython Project [http://www.biopython.org]


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.