ProRule: a new database containing functional and structural information on PROSITE profiles

被引:52
作者
Sigrist, CJA
De Castro, E
Langendijk-Genevaux, PS
Le Saux, V
Bairoch, A
Hulo, N
机构
[1] SIB, CH-1211 Geneva, Switzerland
[2] Univ Geneva, Struct Biol & Bioinformat Dept, Geneva, Switzerland
关键词
D O I
10.1093/bioinformatics/bti614
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. Summary: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains.
引用
收藏
页码:4060 / 4066
页数:7
相关论文
共 11 条
[1]   Swiss-Prot: Juggling between evolution and stability [J].
Bairoch, A ;
Boeckmann, B ;
Ferro, S ;
Gasteiger, E .
BRIEFINGS IN BIOINFORMATICS, 2004, 5 (01) :39-55
[2]   The universal protein resource (UniProt) [J].
Bairoch, A ;
Apweiler, R ;
Wu, CH ;
Barker, WC ;
Boeckmann, B ;
Ferro, S ;
Gasteiger, E ;
Huang, HZ ;
Lopez, R ;
Magrane, M ;
Martin, MJ ;
Natale, DA ;
O'Donovan, C ;
Redaschi, N ;
Yeh, LSL .
NUCLEIC ACIDS RESEARCH, 2005, 33 :D154-D159
[3]   The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 [J].
Boeckmann, B ;
Bairoch, A ;
Apweiler, R ;
Blatter, MC ;
Estreicher, A ;
Gasteiger, E ;
Martin, MJ ;
Michoud, K ;
O'Donovan, C ;
Phan, I ;
Pilbout, S ;
Schneider, M .
NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :365-370
[4]   The disulfide bond pattern of catrocollastatin C, a disintegrin-like/cysteine-rich protein isolated from Crotalus atrox venom [J].
Calvete, JJ ;
Moreno-Murciano, MP ;
Sanz, L ;
Jürgens, M ;
Schrader, M ;
Raida, M ;
Benjamin, DC ;
Fox, JW .
PROTEIN SCIENCE, 2000, 9 (07) :1365-1373
[5]   Disulfide bond assignments of secreted frizzled-related protein-1 provide insights about frizzled homology and netrin modules [J].
Chong, JM ;
Üren, A ;
Rubin, JS ;
Speicher, DW .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (07) :5134-5144
[6]   Automated annotation of microbial proteomes in SWISS-PROT [J].
Gattiker, A ;
Michoud, K ;
Rivoire, C ;
Auchincloss, AH ;
Coudert, E ;
Lima, T ;
Kersey, P ;
Pagni, M ;
Sigrist, CJA ;
Lachaize, C ;
Veuthey, AL ;
Gasteiger, E ;
Bairoch, A .
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2003, 27 (01) :49-58
[7]   The Gene Ontology (GO) database and informatics resource [J].
Harris, MA ;
Clark, J ;
Ireland, A ;
Lomax, J ;
Ashburner, M ;
Foulger, R ;
Eilbeck, K ;
Lewis, S ;
Marshall, B ;
Mungall, C ;
Richter, J ;
Rubin, GM ;
Blake, JA ;
Bult, C ;
Dolan, M ;
Drabkin, H ;
Eppig, JT ;
Hill, DP ;
Ni, L ;
Ringwald, M ;
Balakrishnan, R ;
Cherry, JM ;
Christie, KR ;
Costanzo, MC ;
Dwight, SS ;
Engel, S ;
Fisk, DG ;
Hirschman, JE ;
Hong, EL ;
Nash, RS ;
Sethuraman, A ;
Theesfeld, CL ;
Botstein, D ;
Dolinski, K ;
Feierbach, B ;
Berardini, T ;
Mundodi, S ;
Rhee, SY ;
Apweiler, R ;
Barrell, D ;
Camon, E ;
Dimmer, E ;
Lee, V ;
Chisholm, R ;
Gaudet, P ;
Kibbe, W ;
Kishore, R ;
Schwarz, EM ;
Sternberg, P ;
Gwinn, M .
NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261
[8]   Recent improvements to the PROSITE database [J].
Hulo, N ;
Sigrist, CJA ;
Le Saux, V ;
Langendijk-Genevaux, PS ;
Bordoli, L ;
Gattiker, A ;
De Castro, E ;
Bucher, P ;
Bairoch, A .
NUCLEIC ACIDS RESEARCH, 2004, 32 :D134-D137
[9]   mmsearch:: a motif arrangement language and search program [J].
Junier, T ;
Pagni, M ;
Bucher, P .
BIOINFORMATICS, 2001, 17 (12) :1234-1235
[10]  
Sigrist Christian J A, 2002, Brief Bioinform, V3, P265, DOI 10.1093/bib/3.3.265