Some Useful links:

• Protein Structure Classification

• Web-Tutorials on molecular biology and biochemistry topics:

• Computational Biology and Bioinformatics Tools:

• Networks:

• Molecular docking tools:

• Macromolecular Docking Tools:

• Databases:
• Whole-genome analysis tools:

Protein structure classification

Links to check out and integrate into the list below:

Index of sites offering protein structure classification:

    > www.bioscience.org/urllists/protdb.htm

    > http://www2.ebi.ac.uk/msd/Links/fold.shtml

get reference: Wixon, J. (2001) Structural genomics on the web. Comp. Funct. Genomics 2, 103-113.

Web-Tutorials on molecular biology and biochemistry topics:

• Computational Biology and Bioinformatics Tools:

• Secondary Structure Predictions:
  •     > www.jura.ebi.ac.uk:8888
  •     > www.dot.imgen.bcm.tmc.edu:9331/seq-search/struc-predic.html
  •     > www.gmm.icnet.uk/dsc
  •     > www.cmpharm.ucsf.edu/~nomi/nnpreict.html
  •     > www.pbil.ibcp.fr/NPSA
  •     > www.bmerc-www.bu.edu/psa/index.html
  •     > www.embl-heidelberg.de/argos/predator/predator_info.html
  •     > www.embl-heidelber.de/predictprotein/predictprotein.html
  •     > www.pbil.ibcp.fr/NPSA
  •     > www.doe-mbi.ucla.edu/people/frsvr/frsvr.html

      

• Transmembrane Helices

•     - TMHMM (A. Kdrogh and E. Sonnammer), based on HMM -www.cbs.dtu.dk/krogh/TMHMM
•     - PHDhtm (B. Rost)    > http://dodo.bioc.columbia.edu/predictprotein
•     - Membrane protein explorer    > http://blanco.biomol.uci.edu/mpex

 

• 3d structure Predictions:

•     - Self-correcting distance Geometry (SECODG)
•     - PrISM, protein informatics system for modeling    > http://www.columbia.edu/~ay1/

• Homology modeling:

•     - SWISS-MODEL (automatic homology modeling)    > www.expasy.ch/swissmod/SWISS-MODEL.html
•     - MODBASE, database of comparative models of proteins from complete genomes    > http://guitar.rockefeller.edu/modbase

• Structure Prediction Evaluation

•     - CASP
•     - EVA    > http://cubic.bioc.columbia.edu/eva

• Identification of structural similarity
  •     - DALI, distance matrix alignment    > http://www2.ebi.ac.uk/dali
  •     - SSAP
  •     implemented in CATH, see below
  •     VAST

• Networks:

•     Biochemical networks:    > http://sthenias.cecs.missouri.edu/test_agora/
•     Signaling networks:    > http://icb.mssm.edu/sigpath
•     Protein-protein interaction networks:
•     Regulatory networks:

• Molecular docking tools:

•     - AutoDock    > www.scripps.edu/pub/olson-web/doc/autodock/index.html
•     - DOCK    > www.cmpharm.ucsf.edu/kuntz/dock.html
•     - DockVision    > www.dockvision.com
•     - FlexX    > http://cartan.gmd.de/FlexX
•     - GOLD    > www.ccdc.cam.ac.uk/prods/gold.html
•     - ICM    > www.molsoft.com/icmpages/icmdock.htm
•     - LIGIN    > http://swift.embl-heidelberg.de/ligin
•     - QXP    > ?

• Macromolecular Docking Tools:

•     > www.bmm.icnet.uk

• Databases:
  • Biomedical Publications:

   

  • Genomes:

   

  • Protein sequences:
    •  Swiss-Prot    > www.us.expasy.org./sprot
    •  TrEMBL    > http://www.ebi.ac.uk/trembl/
     
  • Protein families:
    • Curated family databases:
      • Prosite     > www.expasy.ch/prosite
      • Prints     > www.bioinf.man.ac.uk/fingerPRINTScan/bin/atwood/SearchPrintsForm2.pl
      • Pfam    > www.pfam.wustl.edu/hmmsearch.shtml    ,   www.sanger.ac.uk/Pfam/search.shtml

     

    • Clustering databases: 
      • ProDom    > www.toulouse.inra.fr/prodom/doc/blast_form.html
      • DOMO > ?
      • Protomap    > 
      • Prof_pat    > www.mgs.bionet.nsc.ru/mgsprojgrams/prof_pat

     

    • Derived family databases:
      • blocks    > www.blocks.fhcrc.org/blocks_search.html
      • proclass    > http://pir.georgetown.edu/gfserver/gf_intro.html

       

    • Specialized protein family databases:

    GPCR    > www.gpcr.org

    • Specialized protein databases with common properties (not homology):

    Structural database of allergenic proteins    > http://fermi.utmb.edu/SDAP/

     

  • Protein-protein interactions:

    •     - MIPS    > http://mips.gsf.de/proj/yeast/CYGD/interaction/

    •     - DIP, Database of interacting proteins    > http://dip.doe-mbi.ucla.edu/

    •     - Structural database of allergenic proteins (interactions of proteins with IgE)    > http://fermi.utmb.edu/SDAP/

    •     - INTERACT - Protein-Protein Interaction database at The University of Manchester

    •     > http://bioinf.man.ac.uk/resources/interactpr.shtml

    •     - BIND    > http://www.bind.ca/index.phtml?page=databases

    •     - MINT    > http://cbm.bio.uniroma2.it/mint/

    •     - ProNet    > www.doubletwist.com

    •     - PIMRider    > http://pim.hybrigenics.com/pimrider/pimriderlobby/PimRiderLobby.jsp

    •     - KEGG    > http://www.genome.ad.jp/kegg/

    •     - EcoCyc    > http://ecocyc.pangeasystems.com/ecocyc/ecocyc.html

    •     - BBID, Biological Biochemical Image Database    > http://bbid.grc.nia.nih.gov/

    •     - Transpath    > http://www.biobase.de/pages/products/transpath.html

       

     

  • Immune system databases:

    •     - IMGT, International Immunogenetics Database    > http://imgt.cines.fr/

    •     - Structural database of allergenic proteins    > http://fermi.utmb.edu/SDAP/

        

  •     Structures:

     

     

  •     Structural domains:

     

     

  •     Mutational (linked and not linked to disease) databases:

     

        EST, Expressed sequence tags    http://www.ncbi.nlm.nih.gov/About/primer/est.html

     

    • Whole-genome analysis tools:

    • SEALS, http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/index.html;
    • BIOPERL, http://bioperl.org/;
    • EMBOSS, http://www.emboss.org/;
    • META Predict Protein, http://maple.bioc.columbia.edu/~meta/help.html;
    • DAS, http://biodas.org/;
    • ENSEMBL, http://www.ensembl.org/;
    • Genome Explorer, http://www.softberry.com/berry.phtml