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Chapter 11: Making Sense of Proteomics: Using Bioinformatics to Discover a Protein's Structure, Functions, and Interactions—WWW Resources

http://apropos.icmb.utexas.edu/function-prediction.html  Protein Link Explorer (PLEX), University of Texas.

http://bioinfo.pl/cafasp/  CAFASP (Critical Assessment of Fully Automated Structure Prediction).

http://bioinfo.pl/LiveBench/  The Live Bench Project—Continuous benchmarking of protein structure prediction servers.

http://ca.expasy.org/ch2d/  SWISS-2Dpage—Two-dimensional polyacrylamide gel electrophoresis database.

http://ca.expasy.org/sprot/  SWISS-PROT protein knowledgebase.

http://cubic.bioc.columbia.edu/eva/sec/common.html  EVA summary

http://dip.doe-mbi.ucla.edu/  The Database of Interacting Proteins.

http://flybase.bio.indiana.edu/  The FlyBase—A Database of the Drosophila Genome.

http://genome-www5.stanford.edu/cgi-bin/SMD/cluster/QuerySetup.pl  The Stanford Microarray Database.

http://genome-www.stanford.edu/Saccharomyces/  The Saccharomyces Genome Database (SGD).

http://maple.bioc.columbia.edu/pp/submit_meta.html  The META Server.

http://mathbio.nimr.mrc.ac.uk/~rgeorge/snapdragon/  SnapDRAGON domain boundary prediction.

http://nematode.lab.nig.ac.jp/  NEXTDB (The Nematode Expression Pattern DataBase).

http://pfam.wustl.edu/hmmsearch.shtml  Pfam HHM database, Washington University in St. Louis.

http://pipe.rockefeller.edu/modbase-cgi/index.cgi  ModBase—Database of comparative protein structure models.

http://predictioncenter.llnl.gov/  Protein Structure Prediction Center, Lawrence Livermore National Laboratory.

http://prodes.toulouse.inra.fr/prodom/doc/prodom.html  The Protein Domain Database—ProDom.

http://psort.nibb.ac.jp/  PSORT (Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences).

http://rana.lbl.gov/EisenSoftware.htm  The Eisen Lab Software page.

http://scop.berkeley.edu  SCOP (Structural Classification of Proteins).

http://smart.embl-heidelberg.de/  SMART sequence database.

http://transfac.gbf.de/TRANSFAC  TRANSFAC (The Transcription Factor Database).

http://wit.mcs.anl.gov/WIT2/  WIT: Interactive Metabolic Reconstruction.

http://xray.bmc.uu.se/sbnet/prosal.html  ProSal (Protein Sequence Analysis Launcher).

http://www.bind.ca/  The Biomolecular Interaction Network Database (BIND).

http://www.biochem.ucl.ac.uk/bsm/cath/_new/index.html  CATH_Protein Structure Classification.

http://www.blocks.fhcrc.org/blocks_search.html  BLOCKS searcher.

http://www.bmm.icnet.uk/~3djigsaw/dom_fish/  Domain Fishing 1.0.

http://www.bork.embl-heidelberg.de/STRING/  STRING (Search Tool for Recurring Instances of Neighbouring Genes).

http://www.cbs.dtu.dk/services/SignalP/output.html  CBS SignalP V1.1, World Wide Web Prediction Server, Center for Biological Sequence Analysis.

http://www.cifn.unam.mx/Computational_Genomics/regulondb/  RegulonDB v3.2: A Database on Transcriptional Regulation and Genome Organization.

http://www.dkfz-heidelberg.de/abt0135/axeldb.htm  The Axeldb database home page.

http://www.doe-mbi.ucla.edu/Services/moment/  MOMENT Transmembrane Helix Prediction.

http://www2.ebi.ac.uk/dali/fssp/fssp.html  The FSSP database, EMBL-EBI.

http://www.expasy.ch/swissmod/SWISS-MODEL.html  SWISS MODEL.

http://hydra.icgeb.trieste.it/~kristian/SBASE/  BLAST-FTHOM database.

https://www.incyte.com/proteome/databases.jsp  The Proteome BioKnowledge® Library, Incyte Genomics.

http://www.informatics.jax.org/  Mouse Genome Informatics.

http://www.ncbi.nlm.nih.gov  The National Center for Biotechnology Information (NCBI) home page.

http://www.ncbi.nlm.nih.gov/BLAST/  The NCBI BLAST page.

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/altik?gi=115&db=Genome  Escherichia coli K12, complete genome, NCBI.

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/framik?db=G&gi=115  The NCBI Entrez Genome page.

http://www.ncbi.nlm.nih.gov/COG/  The NCBI Clusters of Orthologous Groups of proteins (COGs) page.

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html  The NCBI BLAST Information Guide.

http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/org.html  The NCBI Prominent Organisms Taxonomy/List.

http://www.ncbi.nlm.nih.gov/Structure/dgs/DGSWeb.cgi  The NCBI DGS Algorithm page.

http://www.rcsb.org  Protein Data Bank (PDB).

http://www.sciencemag.org/feature/data/1042937.shl  Hutchison C.A. et al. 1999. Global transposon mutagenesis and a minimal mycoplasma genome.

 
 
 

 
   
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