BioComputing UP Links

Tools:

  • Jalview   -   sequence alignment viewer
  • ESPript   -   sequence alignment printer (e.g. for publications)
  • Jmol   -   protein structure viewer
  • RasMol   -   protein structure viewer
  • PyMol   -   protein structure viewer
  • Cytoscape   -   network analysis and visualization

Databases:

  • Protein Sequence:
    • Genbank   -   DNA sequence database
    • UniProt   -   protein sequence database

    • Pfam   -   protein domain database
    • InterProScan   -   protein domain databse scan

  • Protein Structure:
    • PDB   -   Protein Data Bank
    • CATH   -   structural classification
    • SCOP   -   structural classification
    • PDBSum   -   structural annotation

  • Protein Function:
    • EC-PDB   -   Enzyme Structures Database
    • DHS   -   Dictionary of Homologous Superfamilies
    • GO   -   Gene Ontology

Servers:

  • Sequence Searches:
    • Align   -   Pairwise alignment
    • Water   -   Pairwise local alignment
    • FASTA   -   Database search
    • BLAST   -   Database search
    • CLUSTAL W   -   Multiple alignment

  • 1-D Structure Predictions:
    • Psipred   -   secondary structure prediction
    • Porter   -   secondary structure prediction

    • Disopred   -   disorder prediction
    • CSpritz   -   disorder prediction

    • HMMTOP   -   transmembrane prediction
    • Radar   -   repeat identification
    • ELM   -   Eukaryotic Linear Motifs

  • 3-D Structure Servers:
    • PDB Blast   -   template search
    • Homer   -   homolgy modeling
    • Swiss Model   -   homolgy modeling
    • Meta-Server   -   Fold Recognition

    • CE   -   Structural Comparison
    • ConSurf   -   Structural conservation analysis
    • CASP-8   -   Critical Assessment of techniques for protein Structure Prediction

Institutions:

Local:

Last Updated (Wednesday, 07 October 2009)