Proteins
BIOBASE (MIT only) -- integrated analysis tools coupled with computational and experimental data for drug discovery, biomarker discovery, gene regulation analysis and more.
Protein Data Bank -- tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease
Expert Protein Analysis System (ExPASy) -- portal containing tools and databases for molecular biology analysis.
NCBI
Uniprot -- a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR
Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.
GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.
Nucleic Acids
NCBI
GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.
Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.
EMBL Nucleotide Sequence Database -- Europe's primary nucleotide sequence resource.
Genes and Genomes
Biobase's ExPlain [MIT only] -- biological analysis tool for large-scale data, such as gene expression, proteomics and ChIP-chip data.
Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.
GenePattern -- analysis workflow tool developed to support multidisciplinary genomic research program.
NCBI
UCSD Genome Browser - Bioinformatics and Systems Biology, University of California at San Diego. Projects include genome annotation, protein sequence-structure mapping, functional genomics, reconstruction and modeling of biochemical pathways, infrastructure for biological databases – analysis tools & interfaces.
Ensembl - software system which produces and maintains automatic annotation on selected eukaryotic genomes.
Organisms and Phylogeny
NCBI
MGI: Mouse Genome and Informatics -- international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
SGD: Saccharomyces Genome Database -- contains the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast
Flybase -- contains the Drosophila Genes and Genomes
NIH Rat Genomics and Genetics -- serves as a central point for information on National Institutes of Health (NIH) sponsored and related rat genetic and genomic activities and resources
WormBase -- is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes
ZFIN: The Zebra Fish Model Organism Database -- is a zebrafish model organism database for genetic, genomic and developmental information
Expression
NCBI
Biobase's ExPlain [MIT only] -- biological analysis tool for large-scale data, such as gene expression, proteomics and ChIP-chip data.