Links to search engines for papers

  2. portal to math arXiv.
  3. Knowledge Web (for Medline, etc.)

Links to meetings and societies

  1. Bioinformatics meetings
  2. MIT Bioinformatics Seminar, co-organized by P. Clote (BC) and B. Berger (MIT)

Databases and Tools

  1. LIGSITE: Dresden web site for protein-ligand docking using Connolly surfaces.
  2. HEX: INRIA protein docking software, with associated web server.
  3. GENO3D: Lyon server for protein homology modeling.
  4. Swiss PDB Viewer
  5. Los Alamos National Library HIV sequence database
  6. MicroRNA databases
  7. GRIMM-Synteny
  8. OSfinder
  9. Structure-Interaction Relational Database (SIRD)

RNA tools

  1. LocARNA software for local alignment of RNA, developed by S. Will (Freiburg).
  2. Vienna RNA Package: information on functions, developed by I. Hofacker (Vienna). Also here .
  3. piRNA software from Simon Fraser University to compute partition function for RNA hybridization between two molecules.
  4. RNAalign, paper by G. Blin, A. Denise, S. Dulucq, C. Herrbach, and H. Touzet, with software here.

General links of interest

  1. Valgrind: debugger, manual, info.
  2. JABREF java reference manager.
  3. Ref2Bib reference manager.
  4. Events of the past on certain days of the year.
  5. PyLab
  6. Matplotlib: Python code for 2D plotting
  7. TAZ

Software/Tool Links

  1. myPresto: Tool for structure guided drug development.
  2. SEQATOMs: web service to return sequence, structure, etc. for PDB files that properly treats missing residues. Article by Brandt et al. is here
  3. Numerical software
  4. Gnuplot Tutorial
  5. Python Resources
  6. PyDSTool: Python tool for (differential equation) dynamic systems.


  • Sequence and structure searching site OSfinder
  • Structure-Interaction Relational Database (SIRD)
  • RNA World Website
  • SCOP:Structural Classification of Proteins Database for the Investigation of Sequences and Structures
  • Protein Data Base (Structural)
  • European Bioinformatics Institute (EBI)
  • KEGG:Kyoto Encyclopedia of Genes and Genomes
  • HIV Sequence Database, Los Alamos
  • TIGR Database
  • Church group array data
  • Macromolecular Structures Database
  • EBI Protein topology atlas
  • EMBL WWW Services
  • Metabolic minipathways
  • Spellman yeast cell cycle expression data
  • Protein Domain Database
  • SWEET-DB (Annotated data collections for carbohydrates and LINUCS (Linear notation for unique description of carbohydrate sequences)
  • Gene Expression Links
  • SWISS-PROT (protein sequences) and PROSITE (functional protein sites)
    John C. Weicher, SYSTERS Protein Family Database
  • MIPS yeast pathways
  • GOBASE Organelle Genome Database
  • Saccharomysec Genomic Information Resource
  • BLOCKS Search Server

  • Tools

    1. MINRMS: computing RMSD between proteins.

    Cloaking Link

    1. Link provided by governmental agency for use when anonymously testing web servers when reviewing grant proposals or journal submissions.