Database Catalogs

Helix Systems Scientific Databases - locally available databases (NIH only)
WHALES - Web Homology Alert Service (NIH only)

Genomic

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

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

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

Factors and Motifs

Transfac Professional - transcription activation factor database (NIH only)
BIOBASE - free registration required

Pathways

Reactome - a curated knowledgebase of biological pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes
PID - Pathway Interaction Database, at NCI
BioCyc - Large collection of pathway/genome databases

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

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

Yeast

Saccharomyces Genome Database - at Stanford

Protozoan

PlasmoGF - Plasmodium gene families, at Wenzhou Medical College

Fungi/Mycobacteria

MycoperonDB - Predicted operon and transcriptional units of Mycobacteria

Prokaryote

IECA Database Portal - collection of E. coli servers around the world
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

Other

Ribosomal Database Project - at Michigan State University
National Human Genome Research Institute - ongoing research into genomics