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 Swiss-Prot 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.