References
- H. M. Berman, J. D. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, 'The Protein Data Bank,' Nucleic Acid Research, Vol.28, No.1, pp.235-242, 2000 https://doi.org/10.1093/nar/28.1.235
- Helen B, T. Bhat, Philip B., Zukang F., Gary G., Helge W., and John W., 'The Protein Data Bank and the challenge of structural genomics,' Nature Structural Biology, Vol.7, pp.957-959, 2000 https://doi.org/10.1038/80734
- L. Holm and C. Sander, 'Protein structure comparison by alignment of distance matrices,' Journal of Molecular Biology, Vol.233, pp.123-138, 1993 https://doi.org/10.1006/jmbi.1993.1489
- A. P. Singh and D. L. Brutlag, 'Hierarchical Protein Structure Superposition using both Secondary Structure and Atomic Representations,' Intelligent Systems for Molecular Biology 97, vol.5, pp.284-293, 1997
- A. P. Singh and D. L. Brutlag, Protein Structure Alignment: A Comparison of Methods, 1999
- N. N. Alexandrov and D. Fischer, 'Analysis of topological and nontopological structural similarities in the PDB: New examples with old structures.' Proteins: Structure, Function, and Genetics, Vol.25. No.3, pp.354-365, 1996 https://doi.org/10.1002/(SICI)1097-0134(199607)25:3<354::AID-PROT7>3.3.CO;2-W
- 김진홍, 안건태, 이수현, 이명준, '구조비교를 위한 단백질 데이터의 XML 표현기법', 한국정보과학회 프로그래밍언어연구회, 제16권, 제2호, pp.15-16, 2002
- MGED group, MicroArray and Gene Expression (MAGE), WWW document (http://www.mged.org/Workgroups/MAGE/mage.html), 2004
- BioXML, Genome Annotation Markup Elements (GAME), WWW document (http://www.bioxml.org/Projects/game/), 2003
- V. Guerrini and D. Jackson, 'Bioinformatics and Extended Markup Language (XML),' Online Journal of Bioinformatics, Vol.1, No.1, pp.12-21, 2000
- R. Sayle and E. Milner-White, 'RASMOL: biomolecular graphics for all,' Trends in Biochemical Science, Vol.20, pp.374-376, 1995 https://doi.org/10.1016/S0968-0004(00)89080-5
- P. Bourne, H. Berman, B. McMahon, K.Warenpaugh, J. Westbrook, and P. Fitzgerald, 'The Macromolecular Crystallographic Information File (mmCIF),' Methods In Enzymology. Vol.277, pp.571-590, 1997 https://doi.org/10.1016/S0076-6879(97)77032-0
- Proteomics Inc., BioML:Biological Markup Language, WWW document (http://www.bioml.com/bioml/), 2004
- D. Hanisch, R. Zimmer, and T. Lengauer, 'ProML: the Protein Markup Language for specification of protein sequences, structures and families,' In Silico Biol, Vol.2, No.3, pp.313-324, 2002
- Hofinann K, Bucher P, Falquet L, and Bairoch A (1999) The PROS1TE database, its status in 1999. Nucleic Acids Res 27: 215-219 https://doi.org/10.1093/nar/27.1.215
- P. Murray-Rust and H. Rzepa, 'Chemical markup Language and XML Part 1. Basic principles,' J. Chem. Inf . Comp. Sci, Vol.39, No.6, pp.928-942, 1999 https://doi.org/10.1021/ci990052b
- A. Murzin, S. Brenner, T. Hubbard, and C. Chothia, 'SCOP: A structural classification of proteins database for the investigation of sequences and structures,' Journal of Molecular Biology, Vol.247, pp.536-540, 1995 https://doi.org/10.1006/jmbi.1995.0159
- I. Eidharnmer, I. Jonassen, and W. R. Taylor, Structure Comparison and Structure Patterns, Report no 174, University of Bergen, 1999
- D. S. Greer, J. D. Westbrook, and P. E. Bourne, OpenMMS: An Ontology Driven Architecture for Macromolecular Structure, Objects in Bio and Cheminformatics, 2001
- W3C, Document Object Model (DOM), WWW document (http://www.w3.org/DOM/), 2004
- W. Kabsch and C. Sander, 'Dictionary of Protein Secondary Stucture: Pattern Recognition of Hydrogen-Bonded and Geometrical Features,' Biopolymers, Vol.22, pp.2577-2637, 1983 https://doi.org/10.1002/bip.360221211
- The Apache Software Foundation, Xerces: XML parsers in Java, Apache XML Project, WWW document (http://xml.apache.org/), 2004
- Akmal B. Chaudri, Awais Rashid, Roberto Zicari, XML Data Management: Native XML and XML-Enabled Database Systems, Addison Wesley Professional, 2003
- Martin AC, 'The ups and downs of protein topology: rapid comparison of protein structure,' Protein Eng. Vol.13, No.12, pp.829-837, 2002
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, 'Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,' Nucleic Acids Res., No.25, pp.3389-3402, 1997 https://doi.org/10.1093/nar/25.17.3389
- David W. Mount, Bioinformatics Sequence and Genome Analysis, Gold Spring Harbor Laboratory Press, pp.31-32, 2001
- Su-Hyun Lee, Jin-Hong Kim, Geon-Tae Ahn, and Myung-Joon Lee, 'Efficient Generation of Compatibility Graphs for Two Sets With an Ordered Attribute,' Information Sciences, (submitted), 2004
- Hiroaki KATO and Yoshimasa TAKAHASHI, 'Automated Identification of Three- Dimensional Common Structural Features of Proteins,' J. Chem. Software, Vol.7, No.4, pp.161-170, 2001 https://doi.org/10.2477/jchemsoft.7.161
- Sampo Niskanen, Patrie Ostergard, Cliquer: routines for clique searching, WWW document (http://www.hut.fi/~pat/cliquer), 2002
- VRML Plugin, VRML Plugin and Browser Detector, WWW document (http://cic.nist.gov/vrml/vbdetect.html), 2002
- Sun Microsystems, Java Object Serialization Specification, WWW document (http://java.sun.com/j2se/l.4/docs/guide/serialization/spec/serialTOC.doc.html) 2003
- D. Gilbert, D. Westhead, J. Viksna, and J. Thornton, A computer system to perform structure comparison using TOPS representations of protein structure, Comput. Chem., Vol.26, pp.23-30, 2001 https://doi.org/10.1016/S0097-8485(01)00096-1
- Holm, L., Park, J. DaliLite workbench for protein structure comparison, Bioinformatics, Vol.16, pp.566-567, 2000 https://doi.org/10.1093/bioinformatics/16.6.566