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http://dx.doi.org/10.3745/KIPSTD.2005.12D.2.247

Comparison and Analyzing System for Protein Tertiary Structure Database expands LOCK  

Jung Kwang Su (충북대학교 대학원 전자계산학과)
Han Yu (충북대학교 대학원 전자계산학과)
Park Sung Hee (충북대학교 대학원 전자계산학과)
Ryu Keun Ho (충북대학교 전기전자컴퓨터공학부)
Publication Information
The KIPS Transactions:PartD / v.12D, no.2, 2005 , pp. 247-258 More about this Journal
Abstract
Protein structure is highly related to its function and comparing protein structure is very important to identify structural motif, family and their function. In this paper, we construct an integrated database system which has all the protein structure data and their literature. The structure queries from the web interface are compared with the target structures in database, and the results are shown to the user for future analysis. To constructs this system, we analyze the Flat-File of Protein Data Bank. Then we select the necessary structure data and store as a new formatted data. The literature data related to these structures are stored in a relational database to query the my kinds of data easily In our structure comparison system, the structure of matched pattern and RMSD valure are calculated, then they are showed to the user with their relational documentation data. This system provides the more quick comparison and nice analyzing environment.
Keywords
단백질 구조;단백질 데이터베이스;단백질 구조비교;
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1 A.P.Singh, D.L.Brutlag, 'Hierarchical protein structure superposition using both secondary structure and atomic representations', Bioinformatics, Vol.5, pp.284-293, 1997
2 A.S.Yang, B.Honig, 'An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structuralalignment and a quantitative measure for protein structural distance', J.Mol.Biol, Vol.301, pp.665-678, 2000   DOI   ScienceOn
3 I.Jonassen, I.Eidhammer, D.Conklin, W.R.Taylor, 'Structure motif discovery and mining the PDB', Bioinformatics, Vol.18, pp.362-367, 2002   DOI   ScienceOn
4 I.N.Berezovsky, E.N.Trifonov, 'Protein structure and folding: A new start', Journal of Biomolecular Structure & Dynamics, Vol.19, No.3, 2001   DOI
5 R.SnChez, U.Pieper, F.Melo, N.Eswar, M.A.Mart-Renom, M.S.Madhusudhan, N.Mirkovi and A.ali, 'Protein structure modeling for structural genomics,' Nature Structural Biology, Structural genomics supplements, 2000
6 R.Samudrala, J.Moult, 'A graph-theoretic algorithm for comparative modeling of protein structure', J.Mol.Biol, Vol.279, pp.287-302, 1998   DOI   ScienceOn
7 I.Eidhammer, I.Jonassen, 'Protein structure comparison and structure patterns', ISMB2001 Tutorial, 2001
8 X.Pennec, N.Ayache, 'A geometric algorithm to find small but highly similar 3D substructures in proteins', Bioinformatics, Vol.14, pp.516-522, 1998   DOI   ScienceOn
9 L.P.Chew, D.Huttenlocher, K.Kedem, and J.Kleinberg, 'Fast detection of common geometric substructure in proteins', Journal of Computational Biology, Vol.6, pp.313-325, 1999   DOI   ScienceOn
10 G.M.Maggiora, D.C.Rohrer, J.Mestres, 'Comparing protein structures: A Gaussian-based approach to the three-dimensional structural similarity of proteins', Journal of Molecular Graphics and modeling, Vol.19, pp.168-178, 2001   DOI   ScienceOn
11 C.A.Orengo, A.D.Michie, S.Jones, D.T.Jones, M.B.Swindells, J.M.Thornton, 'CATH - A Hierarchic Classification of Protein Domain Structures', Structure, Vol.5, pp.1093-1108, 1997   DOI   ScienceOn
12 W.Kabsch, C.Sander, 'Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features', Biopolymers, Vol.22, pp.2577-237, 1983   DOI   ScienceOn
13 K.Kedem, L.P.Chew, R.Elber, 'Unit-vectore RMS (URMS) as a tool to analyze molecular dynamics trajectories', Proteins: Structure, Function and Genetics, Vol.37, pp. 554-564. 1999   DOI   ScienceOn
14 J.F.Gibrat, T.Madej, S.H.Bryant, 'Surprising similarities in structure comparison', Curr Opin Struct Biol, Vol.6, pp. 377-385, 1996   DOI   ScienceOn
15 A.Bairoch, R.Apweiler, 'The Swiss-Prot protein sequence data bank and its supplement TrEMBL in 2000', Nucleic Acids Res, Vol.28, pp.45-48, 2000   DOI
16 D.Gilbert, D.Westhead, N.Nagano, J.Thornton. 'Motif-based searching in TOPS protein topology databases', Bioinformatics, Vol.15, pp.317-326, 1999   DOI   ScienceOn
17 C.I.Branden, J.Tooze, 'Introduction to Protein Structure', Garland Publishing, 1991
18 A.M.Lesk, 'Introduction to Protein Architecture: The Structural Biology of Proteins', Oxford Press, 2001
19 N.P.Brown, C.A.Orengo, W.R.Taylor, 'A protein structure comparison methodology', Computers Chem, Vol.20, pp, 359-380, 1996   DOI   ScienceOn
20 H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne, 'The Protein Data Bank', Nucleic Acids Research, Vol.28, pp.235-242, 2000   DOI
21 L.Holm, C.Sander, 'Protein structure comparison by alignment of distance matrices', Biol, Vol.233, pp.123-138, 1993   DOI   ScienceOn
22 R.Brschweiler, 'Efficient RMSD measures for the comparison of two molecular ensembles'. PROTEINS: Structure, Function, and Genetics, Vol.50, pp.26-34, 2003   DOI   ScienceOn
23 I.N.Shindyalov, P.E.Bourne, 'Protein structure alignment by incremental combinatorial extension(CE) of the optimal path', J.Mol.Biol, Vol.233, pp.123-138. 1998   DOI   ScienceOn