Useful links

General Databases

  • UniProt : The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.
  • The Protein Data Bank (PDB) : A single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.

Antimicrobial Peptide Databases

  • AMSDb : Antimicrobial Sequences Database
  • APD : The Antimicrobial Peptide Database
  • CAMP : Collection of Anti-Microbial Peptides
  • APPDb : Antimicrobial Peptide and Protein database (presently inactive).
  • AMPer : A database and discovery tool for antimicrobial peptides, based on hidden Markov models and the SwissProt databank.
  • ANTIMIC : A Singapore Database of antimicrobial peptides.
  • BAGEL : A genome mining tool for putative bacteriocin gene clusters detection.
  • PhytAMP : A database dedicated to plant antimicrobial peptides
  • Peptaibols : Peptaibol Database.
  • Defensins : Defensins Knowledgebase.
  • PenBase : The Shrimp Penaeidin Database.
  • RAPD : A database of recombinantly-produced antimicrobial peptides.
  • SAPD : A database for Synthetic Antibiotic Peptides

Tools

  • Modeller : is used for homology or comparative modeling of protein three-dimensional structures.
  • PyMOL : is a molecular viewer, render tool, and 3D molecular editor.
  • FigTree : FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
  • TreeView : TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.
  • SciDBMaker : SciDBMaker is stand-alone software that allows the extraction of protein data from the UniProt database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases.

Reviews

  • Current trends in antimicrobial agent research: chemo- and bioinformatics approaches: This article reviews progress in the development of computational methods, tools and databases used for organizing and extracting biological meaning from antimicrobial research. Drug Discov Today (2010), 15(13-14):540-6.