--- List of URLs ---

Monday 4 February

Bioinformatics Databases

EMBL (DNA sequence database)

ENTREZ (Search system for sequences and related information, at the NCBI in the States includes Medline)

ExPASy (Comprehensive protein bioinformatics site, and one of the first in the world)

GDB (Mapping information for Human Genome Project)

HGMD (Human Gene Mutation Database)

OMIM (Human genes and linked genetic disorders)

PubCrawler (Alerting service "It goes to the library, you go to the pub!")

The Sanger Centre, UK (Genome sequencing)

SRS (Sequence search and retrieval system, at many sites worldwide this one's at the HGMP in Cambridge, UK)

SRS worldwide public sites list

SwissProt and TrEMBL (Protein sequence databases)

TIGR (The Institute for Genetic Research, USA large scale gene sequencing and functional genomics)

Software and Resources

The Human Genome Mapping Project Resource Centre (HGMP-RC)

EMBnet (general)

IBB, Warsaw (Polish EMBnet node)

EMBOSS (European Molecular Biology Open Software Suite)

JEMBOSS (Graphical user interface to EMBOSS)

Tuesday 5 February

Protein Bioinformatics


ClustalW and Jalview at the EBI







PIX [requires HGMP registration]

Wednesday 6 February

Genomes and Genome Projects

Nature's Genome Gateway

The Sanger Institute: Microbial Genomes

TIGR: Microbial Genomes

Comprehensive Yeast Genome Database

C. elegans Genome Project

Arabidopsis Information Resource

FlyBase: A Database of the Drosophila Genome (at the EBI)

NCBI's Human Genome Resources

GLIMMER (Bacterial/Archael gene finder)

GENSCAN (Eukaryotic gene finder)

NIX [requires HGMP registration]

Ensembl (human genome server)

Artemis (genome annotation tool)

ACT (genome comparison tool)

Protein Structure

The Protein Data Bank (PDB)

Biological Macromolecule Crystallization Database (BMCD)

Molecular Visualisation Freeware (Rasmol and Chime)

Structural Classification of Proteins (SCOP)

The CATH Protein Structure Classification


MRC-LMB: Max Perutz obituary

Thursday 7 February

Protein Modelling

Proteomics Tools at ExPASy

Secondary Structure Prediction: Jpred / Jnet

Transmembrane Helix Prediction: TMPred

David Eisenberg's fold recognition server [Requires free login]

David Jones' fold recognition server (Threader)

Mycobacterium tuberculosis structural genomics consortium homepage

Swiss-Model (free homology modelling server)

MODELLER (homology modelling)

Whatif (relatively cheap, academic modelling program)

"O" (Mainly used in protein crystallography: can be used for modelling. Replaces the classic but obsolete Frodo)

Tripos (manufacturer of commercial modelling software: very expensive)

Accelrys (Formerly MSI; as above)

Procheck (for checking the quality of a structure or model)

Verify-3D (David Eisenberg's web server for structure quality checking)

The CASP protein structure prediction competitions