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Biological Databases:
The following is a list of the biological databases which MIA queries at the present time.
Sequence Data | |
| Database: Description: Website: | PIR Protein Sequence http://www-nbrf.georgetown.edu/pir/ |
|---|---|
| Database: Description: Website: | EMBL DNA Sequence http://www.ebi.ac.uk/ebi_docs/embl_db/ebi/topembl.html |
| Database: Description: Website: | Swiss-Prot Protein Sequence http://www.expasy.ch/sprot/ |
| Database: Description: Website: | GenBank (protein) Protein Query http://www.ncbi.nlm.nih.gov/Entrez/ |
| Database: Description: Website: | TDB (Human) TIGR Human Gene Index http://www.tigr.org |
Structure Data | |
| Database: Description: Website: | EBI MSD Macromolecule File Server Quaternary Structure File http://msd.ebi.ac.uk |
| Database: Description: Website: | PDB Structure Entry http://www.rcsb.org/ |
| Database: Description: Website: | SCOP Structural Classification http://scop.berkeley.edu/ |
| Database: Description: Website: | HSSP Homology Derived Secondary Structure http://www.embl-heidelberg.de/srs5bin/cgi-bin/wgetz?-fun+pagelibinfo+-info+HSSP |
| Database: Description: Website: | DSSP Secondary Structure http://www.embl-heidelberg.de/srs5bin/cgi-bin/wgetz?-fun+pagelibinfo+-info+DSSP |
| Database: Description: Website: | MMDB Structure Summary http://www3.ncbi.nlm.nih.gov/Structure/ |
| Database: Description: Website: | PDBSum Summary of PDB Structure http://www.biochem.ucl.ac.uk/bsm/pdbsum/ |
| Database: Description: Website: | CATH Structural Classification http://www.biochem.ucl.ac.uk/bsm/cath/ |
| Database: Description: Website: | FSSP Structural Family http://www2.ebi.ac.uk/dali/fssp/fssp.html |
| Database: Description: Website: | Sacch3D Protein Structures (Yeast) http://genome-www.stanford.edu/Sacch3D/ |
Visualization | |
| Database: Description: Website: | IMB Jena Image Library Image http://www.imb-jena.de/IMAGE.html |
| Database: Description: Website: | STING Structure and Sequence Browser http://trantor.bioc.columbia.edu/STING/ |
| Database: Description: Website: | GRASS Structure Browser http://trantor.bioc.columbia.edu/GRASS/surfserv_enter.cgi |
| Database: Description: Website: | Columbia Picture Gallery Static Surface Images Generated by GRASP http://trantor.bioc.columbia.edu/GRASS/surfserv_info.cgi#pic_gallery |
| Database: Description: Website: | SEView Feature Table Applet http://www.bioinfo.de/isb/1998/01/0003/main.html |
| Database: Description: Website: | Swiss-3D Image 3D Image http://www.expasy.ch/sw3d/ |
Analysis | |
| Database: Description: Website: | PDBREPORT WHAT CHECK Structure Analysis http://swift.embl-heidelberg.de/pdbreport/ |
| Database: Description: Website: | PROCHECK Structure Summary http://bsmcha1.biochem.ucl.ac.uk/~roman/procheck/procheck.html |
| Database: Description: Website: | PROMOTIF Motif Summary http://www.biochem.ucl.ac.uk/~gail/promotif/promotif.html |
| Database: Description: Website: | ProtParam Physico-chemical Parameters http://www.expasy.ch/tools/ |
| Database: Description: Website: | ProtScale Amino Acid Scale Representation http://www.expasy.ch/www/tools.html |
| Database: Description: Website: | Swiss 2D-PAGE 2D_Gel http://www.expasy.ch/ch2d/ |
Motifs and Domains | |
| Database: Description: Website: | 3Dee Protein Domain Definitions http://barton.ebi.ac.uk/servers/3Dee.html |
| Database: Description: Website: | PROSITE Protein Signature http://www.expasy.ch/prosite/ |
| Database: Description: Website: | PRODOC PROSITE Documentation http://www.expasy.ch/sprot/prosite.html |
| Database: Description: Website: | PRODOM Graphic Ouput of Domain Arrangments http://www.toulouse.inra.fr/prodom/doc/prodom.html |
| Database: Description: Website: | DOMO Domains http://www.infobiogen.fr/~gracy/domo/ |
Literature | |
| Database: Description: Website: | PubMed PubMed Query http://www.ncbi.nlm.nih.gov/Entrez/medline.html |
Miscellaneous | |
| Database: Description: Website: | TOPS Protein Topology Cartoon http://tops.ebi.ac.uk/tops/ |
| Database: Description: Website: | ProtMotDB Domain Movements http://bioinfo.mbb.yale.edu/MolMovDB/ |
| Database: Description: Website: | GeneCensus Genome Occurence of Fold http://bioinfo.mbb.yale.edu/genome/ |
| Database: Description: Website: | Structual Alignments at Yale Structural Alignments of Protein Sequences http://bioinfo.mbb.yale.edu/align/ |
| Database: Description: Website: | PRESAGE Structural Genomics http://presage.berkeley.edu |
| Database: Description: Website: | FlyBase Drosophila Biology http://flybase.bio.indiana.edu |
| Database: Description: Website: | PSI Protein Structure Initiative http://www.structuralgenomics.org |
| Database: Description: Website: | ProClass Family Information http://pir.georgetown.edu/gfserver/proclass.html |
| Database: Description: Website: | MIPS Protein Classification http://speedy.mips.biochem.mpg.de/public/protfam/classification_help.html |
| Database: Description: Website: | Mouse Genome Informatics Genes, Markers and Phenotypes http://www.informatics.jax.org/ |
| Database: Description: Website: | Biochemical Pathways Biochemical Pathways Map http://www.expasy.ch/cgi-bin/search-biochem-index |
| Database: Description: Website: | KEGG Biochemical Pathways Map http://www.genome.ad.jp/kegg/kegg2.html |
| Database: Description: Website: | ENZYME Nomenclature Database Enzyme Class http://www.expasy.ch/enzyme/ |
| Database: Description: Website: | ENZYME Nomenclature Database Enzyme http://www.expasy.ch/enzyme |
| Database: Description: Website: | WIT Alignments and Pathways http://wit.mcs.anl.gov/WIT2/ |
| Database: Description: Website: | NCBI Taxonomy Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html |
| Database: Description: Website: | BLAST BLAST Search http://www.ncbi.nlm.nih.gov/BLAST/ |
| Database: Description: Website: | GeneCards Gene Information http://bioinfo.weizmann.ac.il/cards/ |
| Database: Description: Website: | GDB Gene Entry http://www.gdb.org/ |
| Database: Description: Website: | ProfileScan Profile Search http://www.isrec.isb-sib.ch/index.html |
| Database: Description: Website: | Protomap Family and Cluster Info http://www.protomap.cs.huji.ac.il/ |
| Database: Description: Website: | SWISS-MODEL Strucure Model http://www.expasy.ch/swissmod/SWISS-MODEL.html |
| Database: Description: Website: | HiDB TIGR Haemophilus influenzae DB http://www.tigr.org/tdb/CMR/ghi/htmls/SplashPage.html |
| Database: Description: Website: | MgDB TIGR Mycoplasma genitalium DB http://www.tigr.org/tdb/CMR/gmg/htmls/SplashPage.html |
| Database: Description: Website: | MjDB TIGR Methanococcus jannaschii DB http://www.tigr.org/tdb/CMR/arg/htmls/SplashPage.html |
| Database: Description: Website: | HpDB TIGR Helicobacter pylori DB http://www.tigr.org/tdb/CMR/ghp/htmls/SplashPage.html |
| Database: Description: Website: | AfDB TIGR Archaeoglobus fulgidus DB http://www.tigr.org/tdb/CMR/gaf/htmls/SplashPage.html |
| Database: Description: Website: | TpDB TIGR Treponema pallidum DB http://www.tigr.org/tdb/CMR/gtp/htmls/SplashPage.html |
| Database: Description: Website: | TmDB TIGR Thermotoga maritima DB http://www.tigr.org/tdb/CMR/btm/htmls/SplashPage.html |
| Database: Description: Website: | MtDB TIGR Mycobacterium tuberculosis DB http://www.tigr.org/tdb/CMR/gmt/htmls/LocusNameSearch.html |
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