Wednesday, March 13, 2013

Bioinformatics 101: Protein Analysis

Protein Domain / Structure / Homology Tools:



3D-Structure Viewers:

Mass Spectrometry:
  • PRIDE - mass-spectrometry sample database managed by EMBL-EBI
  • PeptideAtlas - database for mass spectrometry data - includes links to relevant publications
  • MaxQuant - popular tool for mapping proteomics spectra from mass spectrometry data
  • ProteinProphet - another popular tool for mapping proteomics spectra to proteins
  • DanteR - R implementation of the popular DAnTE algorithm for differential expression of mass spectrometry proteomics data
  • LabKey / CPAS - open-source LIMS + basic analysis pipeline
  • PIR - UniProt Protein Information Resource: includes links to databases and peptide mapping tools
Protein-Protein Interaction Databases:
  • IntAct - database for protein-protein interactions
  • BioGRID - database of genetic and protein interactions
  • MINT - protein-protein interaction database
  • STRING - database for known and predicted protein-protein interactions
  • HIPPIE: database of human protein-protein interactions, integrating data from several other databases

Other
  • STITCH: database of drug-protein interactions
  • PaxDb - database of protein expression across different tissues and organisms
  • MOPED - database of protein expression across different tissues and model organisms

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