ProteinCenter User Manual
Table of Contents

Chapter 29. References

UniProt - http://www.ebi.uniprot.org/index.shtml

Apweiler,R., Bairoch,A., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R., Magrane,M., Martin,M.J., Natale,D.A., O'Donovan,C., Redaschi,N. and Yeh,L.S. ( (2004) ) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., , 32, , 115–119

Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S., The Universal Protein Resource (UniProt). Nucleic Acids Res. 33:D154-D159(2005).

INTERPRO - http://www.ebi.ac.uk/interpro/

Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,L., Corpet,F., Croning,M.D. et al. ( (2001) ) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., , 29, , 37–40

ENSEMBL - http://www.ensembl.org/

T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birney Ensembl 2005 Nucl. Acids Res. 2005 33: D447-D453

RefSeq - http://www.ncbi.nlm.nih.gov/RefSeq/

Ref4 - NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Pruitt KD, Tatusova, T, Maglott DR Nucleic Acids Res 2005 Jan 1;33(1):D501-D504

IPI - http://www.ebi.ac.uk/IPI/IPIhelp.html

Kersey P. J., Duarte J., Williams A., Karavidopoulou Y., Birney E., Apweiler R. The International Protein Index: An integrated database for proteomics experiments. Proteomics 4(7): 1985-1988 (2004).

NCBI - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

Wheeler DL et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 33, Database issue D39-D45 (2005)

PDB - http://www.rcsb.org/pdb/

PRF - http://www4.prf.or.jp/en/

DDBJ - http://www.ddbj.nig.ac.jp/

Tateno Y, Saitou N, Okubo K, Sugawara H, Gojobori T. DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D25-8.

Kristensen et al. 2004

Kristensen DB, Brond JC, Nielsen PA, Andersen JR, Sorensen OT, Jorgensen V, Budin K, Matthiesen J, Veno P, Jespersen HM, Ahrens CH, Schandorff S, Ruhoff PT, Wisniewski JR, Bennett KL, Podtelejnikov AV. (2004) Experimental Peptide Identification Repository (EPIR): an integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol Cell Proteomics. 3(10):1023-38

Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium (2000) Nature Genet. 25: 25-29.

IntAct - http://www.ebi.ac.uk/

PrediSi - Hiller K, Grote A, Scheer M, Munch R, Jahn D. 2004, PrediSi: prediction of signal peptides and their cleavage positions. Nucleic Acids Res. 2004; 32:375-9.

Recent evaluation:

Klee EW, Ellis LB.2005; Evaluating eukaryotic secreted protein prediction. BMC Bioinformatics. 2005 Oct 14;6:256.

TMAP from the Emboss package - This program predicts transmembrane segments in proteins, utilising the algorithm described in: "Persson, B. & Argos, P. (1994) Prediction of transmembrane segments in proteins utilising multiple sequence alignments J. Mol. Biol. 237, 182-192."

Gramene - http://www.gramene.org/about/

Gramene: A genomics and genetics resource for rice. Rice Genetics Newsletter, 2006, Vol. 22, No. 1. 9-16.

SGD - http://www.yeastgenome.org/

Hong EL, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane CD, Hitz BC, Miyasato S, Schroeder M, Weng S, Wong ED, Dolinski K, Botstein D, and Cherry JM. "Saccharomyces Genome Database"

ftp://ftp.yeastgenome.org/yeast/

MIPS - http://mips.gsf.de/proj/ppi/

Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D The MIPS mammalian protein-protein interaction database Bioinformatics 2005; 21(6):832-834; [Epub 2004 Nov 5]

FlyBase - http://flybase.bio.indiana.edu/

M.A. Crosby, J.L. Goodman, V.B. Strelets, P. Zhang, W.M Gelbart, and the FlyBase Consortium (2007). FlyBase: genomes by the dozen. Nucleic Acids Research 35: D486-D491; doi:10.1093/nar/gkl827.

TAIR - http://www.arabidopsis.org/

Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Research 2003 31(1):224 Link

emPAI

Yasushi Ishihama, Yoshiya Oda, Tsuyoshi Tabata, Toshitaka Sato, Takeshi Nagasu, Juri Rappsilber, and Matthias Mann, "Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein", Mol. Cell Proteomics 1265-72, 4, 2005. Link

pI

Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. "The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences". Electrophoresis 1993, 14, 1023-1031.

GRAVY

Kyte J, Doolittle RF., "A simple method for displaying the hydropathic character of a protein", J Mol Biol. 1982, 5, 105-32.

KEGG - http://www.genome.jp/kegg/

PlasmoDB - http://plasmodb.org/plasmo/

Aurrecoechea C, et al: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2008 Oct 31.

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18957442

Phenyx - http://www.genebio.com/products/phenyx/