Database Catalogs

Helix Systems Scientific Databases - locally available databases (NIH only)
WHALES - Web Homology Alert Service (NIH only)
J. Craig Venter Institute - formerly TIGR, TCAG, IBEA, and others
GMOD - Generic Model Organism Database project

Genomic

Genomes OnLine Database - Current status of all genomic sequencing projects worldwide
UCSC Genome Browser - the gold standard of genome browsers
National Center for Biotechnology Information (NCBI) - clearinghouse for all genomic information
Ensembl - joint project between EBI and Sanger Institute
GAD - The Genetic Association Database, at NIA
COMPARE - multi organism information system, at the Developmental Biology Institute of Marseille
MINOMICS - facile and in-depth visualization of prokaryotic transcriptomic and proteomic data, at Univ. of Groningen

Nucleic Acids

Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
dbEST - sequence and mapping data on partial, "single-pass" cDNA sequences or ESTs
NDB - Nucleic Acids Database, at Rutgers
Tumor Gene Database - information about targets for cancer-causing mutations
Riboapt DB - Ribozymes & Aptamer Database, at Univ. of Southern Mississippi
SILVA - Quality checked and aligned rRNA sequence data, at Max Planck Institute
ASPicDB - Alternative Splicing Prediction Data Base, at Univ. of Bari
GOfetcher - Complex searching facility for gene ontology, at MCBC

Proteins

SwissProt - at ExPASy.org
Entrez - The Life Sciences Search Engine, at NCBI
SRS - Sequence Retrieval System, at EBI
Molecules To Go - text-based interface to the PDB on Helix Systems
MEROPS - The Peptidase Database, at the Wellcome Trust Sanger Institute
Human Mitochondria l Protein Database - multiple query types available, at NIST
HIV Protease Database - at NCI-Frederick
Human Protein Reference Database - at Johns Hopkins University and the Institute of Bioinformatics
SCOP - Structural Classifications of Proteins
CATH - Hierarchical classification of protein structural relationships
FSSP - Families of structurally similar proteins
PFAM - Database of multiple sequence alignments
GPCRDB - Database of G-protein coupled proteins
ModBase - Database of 3D protein models
HOMSTRAD - Homologous Structure Alignment Database
Database of Macromolecular Movements - with online analysis tools, at Yale Univ.
gpDB - Database of G-proteins and their interactions with GPCRs, at Univ. of Athens
Proteopedia - The Collaborative, 3D Encyclopedia of proteins and other molecules
Microbial Protein Interaction Database - at the J. Craig Venter Institute
OPM - Orientations of Proteins in Membranes Database, at Univ. of Michigan
ModBase - Database of Comparative Protein Structure Models, at UCSF
Protein Ligand Interaction Database - at the Indian Inst. of Chemical Technology, Hyderabad

Factors and Motifs

Transfac Professional - transcription activation factor database (NIH only)
BIOBASE - free registration required
Integrated Transcription Factor Platform - with search capabilities, at Fudan Univ.

Enzymes

REBASE - good old New England Biolabs
ENZYME Database - at ExPASy.org
IntEnz - at EBI
Biology-oriented newsgroups - at Indiana University
CATRES - Database of catalytic residues, at EBI
CSA - Catalytic Site Atlas, at EBI

Plasmids

Genome Database of Naturally Occurring Plasmids - 'nuff said

Organism-Specific Databases

Mammalian

Mouse Genome Database - synoptic descriptions with bibliographic citations
Portable Dictionary of the Mouse Genome - compact, downloadable database
Rate Genome Database - at the Medical College of Wisconsin
HumanCyc - Encyclopedia of Homo sapiens Genes and Metabolism
MouseNet - Predict functional assignments and network components for mouse genomes, at Princeton Univ.

Vertebrate

Zebrafish Model Organism Database - at the University of Oregon

Worm

Worm Base - biology and genome of C. elegans
Caenorhabditis elegans WWW Server - one-stop shopping for C. elegans

Insect

FlyBase - comprehensive database for genetics and molecular biology of Drosophila

Other invertebrates

SpBase - Sea Urchin Genome Database, at CalTech

Yeast

Saccharomyces Genome Database - at Stanford
Candida Genome Database - from NIDCR and Stanford Univ

Protozoan

PlasmoGF - Plasmodium gene families, at Wenzhou Medical College
dictyBase - our friend the amoeba
ParameciumDB - A database for Paramecium tetraurelia, at CNRS

Fungi/Mycobacteria

MycoperonDB - Predicted operon and transcriptional units of Mycobacteria
spolTools - tools to browse and analyze spoligotype data of Mycobacterium tuberculosis, at Univ. of New South Wales

Prokaryote

IECA Database Portal - collection of E. coli servers around the world
EcoCyc - Encyclopedia of Escherichia coli K-12 Genes and Metabolism
SubtiList WWW Server - all about B. subtilis, Pasteur Institute
Entrez Microbial Genomes - 348 completed genomes and counting...
BAGET - very nice tool for getting sequence & info from prokaryotic genomes, from Université Paris

Plants

Arabidopsis Information Resource - very nice gateway to our favorite mustard weed
Grain genes - database for triticaea and avena
The Korea Rice Genome Database - at Myongii University
ChromDB - the plant chromatin database, at University of Arizona
SoyBase - all about Glycine max
Maize Genetics and Genomics Database - all about Zea mays, supported by the USDA ARS
Barley Genetic Stocks Database -
GRAMENE - A Resource for Comparative Grass Genomics
Sol Genomics Network - Solanaceae sp. (tomato, potato, tobacco, eggplant, etc.), at Cornell Univ.
Osiris - visualization and data mining of Oryza sativa promoter sequences, at Washington State Univ.
AtREA - Arabidopsis thaliana regulatory element analyzer, at Univ. of Calcutta

Other

Ribosomal Database Project - at Michigan State University
National Human Genome Research Institute - ongoing research into genomics
VectorBase - Invertebrate Vectors of Human Pathogens
GeneDB - curated pathogen genomes, from the Sanger Institute
varDB - Pathogen-specific database of antigenic variation, at Kyoto Univ.