一、主要数据库

UniProtKB :蛋白质功能数据库

UniProtKB/Swiss-Prot：蛋白序列数据库

STRING：蛋白相互作用数据库

SWISS-MODEL Repository：蛋白结构相似模型数据库（protein structure homology models ）

PROSITE ：蛋白结构域及家族数据库

ViralZone • portal to viral UniProtKB entries

生化大分子数据库：

RSCB；MMDB；PDBe；BMRB； SBKB；ModBase SCOP；CATH

Prosite ： 蛋白质结构域、家族及功能位点数据库

PRINTS – 蛋白印记数据库

BLOCKS - A database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins

CDD – 蛋白保守结构域数据库

ProDom – 蛋白结构域家族数据库

PFam – 蛋白结构域数据库.

HPA – 人蛋白质数据库。

neXtProt ：人类蛋白数据库

GlyTouCan ：国际多聚糖结构数据库

GPSDB ：基因与蛋白同义数据库(gene and protein synonyms)

HAMAP ：UniProtKB 家族分类和注释数据库

MatrixDB ：蛋白-多聚类相互作用数据

MetaNetX ：代谢网路数据分析数据库。

MyHits ：蛋白结构域数据库

PaxDb ：蛋白质在物种种丰度数据库。

Prolune ：蛋白科学文献数据库 (in French) 

Protein Model Portal ：蛋白结构信息数据库

Protein Spotlight：关于蛋白的文献综述数据库

Rhea ：专家验证过的生化反应数据库

SugarBind：pathogen sugar-binding

SWISS-2DPAGE ：proteins on 2-D and SDS PAGE maps

SwissBioIsostere： bioIsosteres for small molecules

SwissLipids：已知的关于脂质的数据资源

SwissPalm：棕榈酰化数据库

SwissSidechain • non-natural amino-acid sidechains

TCS ：interaction specificity in two-component systems

UniCarb-DB： glycan mass and structural data

UniCarbKB：验证过的glycan数据库

UniPathway：UniProtKB 代谢通路数据库

World-2DPAGE Constellation：2D PAGE资源

World-2DPAGE Repository：gel-based proteomics data

二、常用工具功能及网站

Function: Prediction of leucine zipper domains

Website: http://2zip.molgen.mpg.de/index.html

Function: find user-defined patterns in protein sequences

Website: http://www.dkfz.de/mga2/3of5/3of5.html

Function: protein identification by aa composition

Website: http://web.expasy.org/aacompident

Function: amino acid composition comparison

Website: http://web.expasy.org/aacompsim/

Function: Prediction of the helical content of peptides

Website: http://agadir.crg.es/

Function: simulation of genome evolution

Website: http://www.cbrg.ethz.ch/alf

Function: Four tools for multiple alignments

Website: http://coot.embl.de/Alignment/

Function: protein sequences comparisons

Website: http://www.cbrg.ethz.ch/services/AllAll

Function: Advanced Protein Secondary Structure Prediction

Website: http://imtech.res.in/raghava/apssp/

Function: Molecular modeling software

Website: http://www.biomolecular-modeling.com/Products.html

Function: predict GPI modification sites

Website: http://mendel.imp.ac.at/sat/gpi/gpi_server.html

Function: Biochemical Pathways

Website: http://web.expasy.org/pathways/

Function: sequence similarity search

Website: http://web.expasy.org/blast/

Function: BLAST search on the UniProt web site

Website: http://www.uniprot.org/blast

Function: Biological sequence similarity search

Website: http://www.ncbi.nlm.nih.gov/BLAST/

Function: BLAST search on protein sequence databases

Website: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_blast.html

Function: Blast to Fasta conversion

Website: http://imed.med.ucm.es/Tools/blast2fasta.html

Function: MSA pretty printer

Website: http://embnet.vital-it.ch/software/BOX_form.html

Function: Protein secondary structure prediction

Website: http://www.biogem.org/tool/chou-fasman/

Function: chloroplast transit peptides & cleavage sites

Website: http://www.cbs.dtu.dk/services/ChloroP/

Function: Directory of computational drug design tools

Website: http://www.click2drug.org/

Function: Align two or more protein sequences

Website: http://www.uniprot.org/align

Function: Multiple sequence alignment

Website: http://embnet.vital-it.ch/software/ClustalW.html

Function: Multiple sequence alignment program

Website: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html

Function: Multiple sequence alignment program

Website: http://www.ebi.ac.uk/Tools/msa/clustalw2/

Coiled-Coils prediction

Function: Prediction of coiled coils regions

Website: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_lupas.html

Function: Prediction of Coiled Coil Regions in Proteins

Website: http://embnet.vital-it.ch/software/COILS_form.html

Function: Color Protein Sequence

Website: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_color.html

Function: theoretical pI and Mw computation

Website: http://web.expasy.org/compute_pi/

Function: Protein homology modeling

Website: http://www.cbs.dtu.dk/services/CPHmodels/

Function: Prediction of palmitoylation sites in proteins

Website: http://csspalm.biocuckoo.org/

Function: Prediction of transmembrane regions

Website: http://mendel.imp.ac.at/sat/DAS/DAS.html

Function: Sequence redundancy reduction

Website: http://web.expasy.org/decrease_redundancy/

Function: Local multiple sequence aligment

Website: http://bibiserv.techfak.uni-bielefeld.de/dialign/

Function: GlcNAc O-glycosylation sites in D.discoideum

Website: http://www.cbs.dtu.dk/services/DictyOGlyc/

Function: Prediction of disordered protein regions

Website: http://dis.embl.de/

Function: Domain linker predictor

Website: http://www.tuat.ac.jp/~domserv/cgi-bin/DLP-SVM.cgi

Function: sequence similarity plots

Website: http://myhits.isb-sib.ch/cgi-bin/dotlet

Function: Eukaryotic Linear Motifs

Website: http://elm.eu.org/

Function: bioinformatics tools, databases and courses

Website: http://embnet.vital-it.ch/

EMBOSS translation tools

Function: sequence translation tools

Website: http://www.ebi.ac.uk/Tools/st/

Function: Identification of PEST motifs

Website: http://emboss.bioinformatics.nl/cgi-bin/emboss/epestfind

FASTA/SSEARCH/GGSEARCH/GLSEARCH

Function: Sequence similarity searching of protein db

Website: http://www.ebi.ac.uk/Tools/sss/fasta/

Function: protein post-translational modification prediction

Website: http://web.expasy.org/findmod/

Function: peptide identification from unspecific cleavage

Website: http://web.expasy.org/findpept/

Function: scan sequences against PRINTS 

Website: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/fingerPRINTScan/FPScan_fam.cgi

Function: Sequence-structure homology recognition

Website: http://tardis.nibio.go.jp/fugue/

Function: RNA/DNA & Amino Acid Sequence Logos

Website: http://www.biogenio.com/logo/

Function: Protein molecular modelling

Website: http://geno3d-pbil.ibcp.fr/cgi-bin/geno3d_automat.pl?page=/GENO3D/geno3d_home.html

Function: Protein disorder/globularity/domain predictor

Website: http://globplot.embl.de/

Function: oligosaccharide structure mass calculation

Website: http://web.expasy.org/glycanmass/

Function: exoglycosidase digestion of glycans

Website: http://glycoproteome.expasy.org/glycodigest/

Function: visual browser for glycoproteomic data

Website: http://glycodomain.glycomics.ku.dk/

Function: oligosaccharide structure prediction

Website: http://web.expasy.org/glycomod/

Function: alignment of sequences around glycosylation sites

Website: http://glycoproteome.expasy.org/glycositealign/

Function: visualize a set of glycan structures

Website: http://www.glycoviewer.babs.unsw.edu.au/

Function: network of glycoepitopes

Website: http://glycoproteome.expasy.org/epitopes/

Function: glycan sub-structure search

Website: http://glycoproteome.expasy.org/substructuresearch

Function: Protein secondary structure prediction

Website: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html

Function: identify GPI-anchor signals

Website: http://gpi.unibe.ch/

Function: protein physical and chemical parameters

Website: http://www.alphalyse.com/gpmaw_lite.html

Function: Prediction of kinase-specific phosphorylation site

Website: http://gps.biocuckoo.org/

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