蛋白质生物信息分析
基本性质分析: /protparam/
参考文献:Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.;
Protein Identification and Analysis Tools on the ExP ASy Server;
(In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005).
pp. 571-607
翻译后修饰：
信号肽预测http://www.cbs.dtu.dk/services/SignalP-3.0/
残基磷酸化预测：http://www.cbs.dtu.dk/services/NetPhos/
跨膜结构预测：http://www.cbs.dtu.dk/services/TMHMM-2.0/
http://bp.nuap.nagoya-u.ac.jp/sosui/
http://www.sbc.su.se/~miklos/DAS
亚细胞定位：http://www.cbs.dtu.dk/services/TargetP/
http://psort.hgc.jp/
1一级结构分析：/protscale/
1二级结构分析：http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html Significant improvement in protein secondary structure prediction by consensus prediction from multiple alignments., Cabios (1995) 11, 681-684
Network Protein Sequence Analysis
TIBS 2000 March V ol. 25, No 3 [291]:147-150
1二级结构预测：http://www.cbs.dtu.dk/services/CPHmodels/
CPHmodels-3.0 - Remote homology modeling using structure guided sequence profiles Nielsen M., Lundegaard C., Lund O., Petersen TN
Nucleic Acids Research, 2010, Vol. 38, doi:10.1093/nar/gkq535
View the abstract.
CPHmodels 2.0: X3M a Computer Program to Extract 3D Models.
O. Lund, M. Nielsen, C. Lundegaard, P. Worning
Abstract at the CASP5 conference A102, 2002.
三级结构：http://geno3d-pbil.ibcp.fr/
/workspace/index.php?func=modelling_simple1
参考文献：
Bulfer, S.L., Scott, E.M., Couture, J.F., Pillus, L., Trievel, R.C. Crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis. (2009) J.Biol.Chem.284: 35769-35780
Benkert P, Biasini M, Schwede T. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics, 27(3):343-50.
Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for
protein structure homology modeling. Bioinformatics, 22,195-201.
•
Schwede T, Kopp J, Guex N, and Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server.
Nucleic Acids Research 31: 3381-3385.
•
Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein
modeling. Electrophoresis 18: 2714-2723.
3D结构：http://www.cbs.dtu.dk/services/FeatureMap3D/
FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
Rasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stærfeldt, Peter Wad Sackett, and Anne Mølgaard.Nucl. Acids Res. 2006 34: W84-W88
2生物功能位点：
/InterProScan/
参考文献：
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
(1997 Sep 01) Nucleic acids research 25 (17) :3389-402
Basic local alignment search tool.
(1990 Oct 05) Journal of molecular biology 215 (3) :403-10
/scanprosite/
线性抗原表位预测：/scripts/MHCServer.dll/home.htm
MOTIF:
/meme/cgi-bin/meme.cgi
参考文献：
Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.。