E-MSD: an integrated data resource for bioinformatics

被引：62

作者：

Golovin, A ^{[1
]}

Oldfield, TJ ^{[1
]}

Tate, JG ^{[1
]}

Velankar, S ^{[1
]}

Barton, GJ ^{[1
]}

Boutselakis, H ^{[1
]}

Dimitropoulos, D ^{[1
]}

Fillon, J ^{[1
]}

Hussain, A ^{[1
]}

Ionides, JMC ^{[1
]}

John, M ^{[1
]}

Keller, PA ^{[1
]}

Krissinel, E ^{[1
]}

McNeil, P ^{[1
]}

Naim, A ^{[1
]}

Newman, R ^{[1
]}

Pajon, A ^{[1
]}

Pineda, J ^{[1
]}

Rachedi, A ^{[1
]}

Copeland, J ^{[1
]}

Sitnov, A ^{[1
]}

Sobhany, S ^{[1
]}

Suarez-Uruena, A ^{[1
]}

Swaminathan, GJ ^{[1
]}

Tagari, M ^{[1
]}

Tromm, S ^{[1
]}

Vranken, W ^{[1
]}

Henrick, K ^{[1
]}

机构：

[1] European Bioinformat Inst, EMBL Outstn, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2004年 / 32卷

关键词：

D O I：

10.1093/nar/gkh078

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD,atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples show-casing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow-tutorial/).

引用

页码：D211 / D216

页数：6

共 14 条

[1] The ENZYME database in 2000 [J].

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305

[2]

BAIROCH A, 1994, NUCLEIC ACIDS RES, V22, P3578

[3]

Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkr1065, 10.1093/nar/gkh121]

[4] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[5] E-MSD: the European Bioinformatics Institute Macromolecular Structure Database [J].

Boutselakis, H ;

Dimitropoulos, D ;

Fillon, J ;

Golovin, A ;

Henrick, K ;

Hussain, A ;

Ionides, J ;

John, M ;

Keller, PA ;

Krissinel, E ;

McNeil, P ;

Naim, A ;

Newman, R ;

Oldfield, T ;

Pineda, J ;

Rachedi, A ;

Copeland, J ;

Sitnov, A ;

Sobhany, S ;

Suarez-Uruena, A ;

Swaminathan, J ;

Tagari, M ;

Tate, J ;

Tromm, S ;

Velankar, S ;

Vranken, W .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :458-462

[6] The gene ontology annotation (GOA) project: Implementation of GO in SWISS-PROT, TrEMBL, and InterPro [J].

Camon, E ;

Magrane, M ;

Barrell, D ;

Binns, D ;

Fleischmann, W ;

Kersey, P ;

Mulder, N ;

Oinn, T ;

Maslen, J ;

Cox, A ;

Apweiler, R .

GENOME RESEARCH, 2003, 13 (04) :662-672

[7] Searching the medical literature using PubMed: A tutorial [J].

Ebbert, JO ;

Dupras, DM ;

Erwin, PJ .

MAYO CLINIC PROCEEDINGS, 2003, 78 (01) :87-91

[8] The PROSITE database, its status in 2002 [J].

Falquet, L ;

Pagni, M ;

Bucher, P ;

Hulo, N ;

Sigrist, CJA ;

Hofmann, K ;

Bairoch, A .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :235-238

[9]

FUA YH, 1999, IEEE P INF VIS 99, P58

[10] AstexViewer™:: a visualisation aid for structure-based drug design [J].

Hartshorn, MJ .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2002, 16 (12) :871-881

← 1 2 →