Proteomics Resources for HIV Research

The BioAfrica Proteomics Resource has been created to direct HIV clinicians and scientists to data and tools available for both protein sequence and protein structure analyses of HIV. This page contains an introductory-level list of tools and databases.

Protein Databases: 
  • UniProt - the central repository of protein sequence and function data, created by combining the information contained in Swiss-Prot, TrEMBL, and PIR
  • DSSP - Database of Secondary Structure
  • SCOP - Structural Classification Of Protein
  • PDB - Protein structure Data Bank [Molecules R Us | PDBsum]
Specialized Viral Protein Databases: 
  • VOG - Viral Clusters of Orthologous Groups of proteins at NCBI.
  • dbMHC - Major Histocompatibility Complex database at NCBI
  • MEROPS - Peptidase database.
  • HIV Drug Resistance Database - All published drug-related variations in Protease and Reverse Transcriptase
Motif and Transcription Factors Databases: 
  • Pfam - Protein Family classification
  • ProDom - Protein Domain database
  • MOTIF - Dictionary of Protein Sites and Patterns
  • PROSITE - Protein Motif Fingerprint Database
Proteomics Site Map, with external links to main databases and tools

Proteomics site map, with external links to main databases and tools.

Protein Sequence Database of functionally annotated protein sequences - PIR Protein Motif Fingerprint Database - PROSITE Molecular Modelling Database at NCBI - Entrez Structure Protein Data Bank of 3D structures - PDB Curated Protein sequence database - SwissProt
Protein sequence similarity searches: 
  • BLAST (HIV, SIV, HCV and HBV) - Protein sequence comparison tool that implements a Heuristic algorithm - BioAfrica
  • PSI-BLAST - Position Specific Iterated BLAST - NCBI
  • MPsrch - Protein sequence comparison tool that implements true Smith & Waterman exhaustive algorithm
Protein sequence alignment: 
  • ClustalW - Produces multiple sequence alignments
  • TCoffee - More accurate than ClustalW for sequences with <30% identity
  • MultAlin - Global similarity multiple sequence alignment using hierarchical clustering
  • Dotlet - Dot Matrix sequence comparison
Protein sequence prediction tools: 
  • PA-IBM - Protein annotation tool, searches SwissProt/TrEMBL for similar proteins, and provides predicted functional regions
  • N-Glycosite - Predict potential N-glycosylation sites in an aligned set of protein sequences
  • NetPhos - Prediction of Ser, Thr and Tyr phosphorylation sites
  • PeptideCutter - Predicts potential cleavage sites
Protein sequence analysis/manipulation: 
  • GENIO/logo - Colour sequences based on specified characteristics and analyze amino acid replacement and distribution
  • ProtParam - Calculate physico-chemical parameters of a protein sequence
  • Backtranslation - Translates a protein sequence back to a nucleotide sequence
  • ReadSeq - Convert between sequence file formats

Protein structure analysis: 

  • SWISS-MODEL - Automated knowledge-based protein structure prediction server
  • PredictProtein - Gateway to multiple prediction servers (secondary structure, membrane regions, homology modelling and threading)
  • SMART - Simple Modular Architecture Research Tool
  • PINTS - Patterns In Non-homologous Tertiary Structures (finds clusters of functionally relevant amino acids)
Molecular Modelling tools: 
  • DOCK - Characterization of binding site.
  • AutoDock - Docking of flexible ligands into receptor binding sites.
  • DOT - Rigid body protein-protein docking
Tutorials:  Downloads: 
  • Cn3D (Linux, PC, Mac, Unix) - NCBI - Simultaneously displays structure, sequence, annotation and alignment data
  • SwissPDB Viewer  (Linux, PC, Mac, Unix) - Expasy - Analyze proteins structures, with the ability to deduce structural alignments, mutate amino acids, and perform molecular surface calculations, homology modelling and energy minimization calculations.

Page last updated by Tulio de Oliveira.