Basic Science/Molecular Biology/Research Resources
Protein Analysis Databases
UCSC Genome Bioinformatics – "contains the reference sequence and working draft assemblies for a large collection of genomes"
EBML-EBI Protein Databases – houses many protein related databases
EBI Integr8 – "deciphered genomes and their corresponding proteomes"
EBI MPsrch – "biological sequence comparison tool"
EBI ClustalW – "multiple sequence alignment program for DNA or proteins"
EBI T-Coffee – "combine results obtained with several alignment methods. For instance if you have an alignment coming from ClustalW2, an other alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement with all these methods."
EBI InterProScan Sequence Search – "identifies distant relationships in novel sequences… used for classification of protein sequences"
NCBI Protein BLAST – "finds regions of similarity between biological sequences"
BLink - "Pre-computed sequence alignments, generated from routine all-against-all BLAST comparisons performed at NCBI, are available for each protein record in Entrez. The best 200 of these alignments can be displayed by clicking on the "BLink" link in the upper right-hand corner of Entrez protein reports."
NCBI Conserved Domain Database (CDD) – "used to identify the conserved domains present in a protein query sequence"
ExPASy Proteomics Tools
Search Tool for the Interacting Genes/Proteins (STRING) – proteins and their interactions
Scansite (MIT) – "Scansite works best with standards-compliant browsers, such as Firefox, Mozilla, Netscape, Opera, Galeon, Safari, and Konqueror. Internet Explorer users may have problems and are encouraged to use an alternative."
DNA Analysis Databases
NetPrimer – primer analysis
Primer3Plus – choose primers for DNA analysis
NEBcutter – "take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once."
Webcutter – restriction mapping
READSEQ – sequence conversion
NCBI Map Viewer – "search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest."
Ensembl Genome Browser – "produces and maintains automatic annotation on selected eukaryotic genomes"
UniProt – "central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR."
Human Protein Reference Database (HPRD) – "entralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome."
GenBank – "genetic sequence database, an annotated collection of all publicly available DNA sequences"
RefSeq – "provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products. RefSeq is a baseline for medical, functional, and diversity studies"
HomoloGene – "system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes"
Genome Resource Guides - Access to genome resource guides for selected organisms.
GeneCards – "includes automatically-mined genomic, proteomic and transcriptomic information, as well as orthologies, disease relationships, SNPs, gene expression, gene function, and service links for ordering assays and antibodies"
European Bioinformatics Institute - The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
ClusterMed – powered by the Vivisimo, it organizes PubMed results into meaningful categories.
Molecular Biology Collections
Penn State Academic Information Research Tools - compiled by the Research Department
Biology Browser - search by organism, subject, and geography
BioToolKit - bioinformatics and neuroinformatics resources for the analysis and visualization of the genome, transcriptome, and proteome, and to neuroinformatics tools enabling visualization of neuroanatomic structure.
ExPASy Life Sciences Directory - portal with molecular biology databases
Genamics - portal with information from biochemistry to sequence presentation
Infomine - Biological Agricultural and Medical Science
Molecular Biology Gateway - Books to purchase from Horizon Press, links to other resources
BIOSCI/BIONET - news and information
PDB Protein Data Bank - The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.
Molecular Visualization Freeware - RasMol from the University of Massachusetts
Swiss PDB Viewer - Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.
Kinemage - 3D interactive graphics (Duke University)
Molecular Modeling DataBase (MMDB) - "structure database is a subset of three-dimensional structures obtained from the Protein Data Bank excluding theoretical models. MMDB is a database of ASN.1-formatted records, is capable of archiving conventional structural data as well as future descriptions of biomolecules, such as those generated by electron microscopy."
University of Washington Funding Resources - Research funding portal