Bioinformatics & Genomics
Courses, Journals, Definitions
Portals & Comprehensive Servers
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3 Dee - Database of Protein Domain Definitions
[European Bioinformatics Institute] 3Dee contains structural domain definitions for all protein chains in the Protein Databank (PDB) [EBI-MSD/RCSB] that have 20 or more residues and are not theoretical models.
[EMBL] A database of aligned protein structures and related sequences.
[Univ. of Wisconsin] "A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Amino Acids." The database includes information on each biological molecule, NMR spectral parameters, kinetics, thermodynamics,and structure.
Blocks WWW Server
[Fred Hutchinson Cancer Research Center] Tools for the detection and verification of protein sequence homology.
CAME: Center of Applied Molecular Engineering
[Institute of Chemistry and Biochemistry, University of Salzburg] CAME offers a variety of internet services such as: a protein structure superimposition server [ProSup], the structural genome annotation for C. elegans [WILMA], and a protein structure analysis tool [PROSAII].
CATH Protein Structure Classification
[Univ. College, London] A novel hierarchical classification of protein domain structures, which clusters proteins at four levels: class, architecture, topology, and homologous superfamily.
Clusters of Orthologous Groups
[NCBI] (COGs) A phylogenetic database (with a comparison search server incorporated) of orthologous proteins in many complete genomes.
CMS Molecular Biology Resource
[San Diego Supercomputer Center] A compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Moldeling.
[EBI] Service for comparing protein structures in 3D. Protein structure coordinates are submitted for comparison against entries in the Protein Data Bank.
Database of Secondary Structure in Proteins
[EBI] (DSSP) The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).
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DNA Binding Protein Structural Families
[Univ. College London] "These Web pages include a structural classification of all protein-DNA complexes solved by X-ray crystallography to a
resolution of 3.0 angstroms or better as of 4th January 2000."
[Gis Infobiogen, Gracy/Argos] A database of homologous protein domain families obtained from successive sequence analysis steps including similarity search, domain delineation, multiple sequence alignment, and motif construction.
[Centre for DNA Fingerprinting and Diagnostics] The Database of Structural Motifs in Proteins contains a representative protein data set derived using the PDB_SELECT program, where 1351 chains with 228325 residues were obtained using a 25% threshold on the PDB release 2000 and all the proteins in the PDB.
[Stanford Univ.] A protein identification tool allowing a protein sequence to be entered and submitted for identification.
[National Center for Biotechnology Information] Provides a General search for nucleotide sequences, protein sequences, biomolecule 3D structures, genomes, taxonomy or literature.
Enzyme Structures Database
[University College London] A database of the known enzyme structures in the Brookhaven Protein Data Bank.
FSSP: Fold classification based on Structure-Structure alignment of Proteins
[European Molecular Biology Laboratory] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
FSSP ftp Site
[EBI] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
GeneFIND: Gene Family Identification Network Design
[Protein Information Resource] A database search system combining search/alignment tools and the ProClass database. Output includes global and motif scores, alignments to the best-matched members of the Pro-Site protein groups and PIR superfamilies, motif pattern matches, and links to the corresponding ProClass family records.
[European Bioinformatics Institute] "GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases."
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[Gladstone Institutes, UCSF] GenMAPP is a free computer application designed to visualize gene
expression data on maps representing biological pathways and groupings
G-Protein Coupled Receptor Database: GPCR 3D Models
[European Molecular Biology Laboratory] Database of atomic coordinates of 3D models of G-protein coupled receptors.
[NHGRI] An annotated collection of non-redundant protein sequences, three-dimensional structures, and genomic information for the homeodomain protein family.
HOMSTRAD: Homologous Structure Alignment Database
[University of Cambridge] Database provides aligned three-dimensional structures of homologous proteins.
HSSP: Homology-derived Secondary Structure of Proteins
[EMBL] A database of homology-derived secondary structure of proteins created by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile.
LAMA: Local Alignment of Multiple Alignments
[Fred Hutchinson Cancer Research Center] This program compares multiple protein sequence alignments with each other. The program can search databases of such multiple alignments. The search is for sequence similarities between conserved regions of protein families.
Library of Protein Family Cores
[The Helix Group at Stanford University] A library useful for building models, threading, and exploring analysis. Contains structural alignments of protein families and computed average core structures for each family.
[Incyte Gemomics] LifeSeq provides fee access to Incyte's human gene sequence databases, complete with integrated bioinformatics tools.
Links to Pathway and Other Databases
[GenomeNet] A comprehensive list of links to biological and biochemical databases. The types of databases include: metabolic pathways; enzymes, compounds, and elements; regulatory pathways; protein-protein interactions; nomenclature and classification; taxonomy; and complete genomes and analysis.
Links to Pathway Databases
[Kyoto University] A list of links to databases of pathways of reactions & compounds in living cells.
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[Munich Information Centre for Protein Sequences] A multi-database information retrieval program specifically designed to access macromolecular sequence databases.
MMDB: Molecular Modeling Database
[Entrez at NCBI] A compilation of all the Brookhaven Protein Data Bank 3-dimensional structures of biomolecules from crystallographic and NMR studies. Structures in MMDB have been compared with one another using VAST (Vector Alignment Search Tool).
[Rockefeller University] Database of comparative protein structure models.
Molecular Sequence Megaclassification
[Washington Univ., St. Louis] Provides access to a non-redundant molecular sequence collection that can be accessed by domain type of sequence.
Molecules R US
[NIH] A WWW Forms interface which facilitates access (browsing, searching and retrieval) to the molecular structure data contained within the Brookhaven Protein Data Bank (PDB).
NRL_3D Sequence-Structure Database
[Protein Information Resource] A sequence-structure database derived from the Brookhaven Protein Data Bank.
[Weizmann Institute] OCAŠ is a browser/database for retrieving rich content annotation on structure and function for proteins found in the Protein Data Bank.
[Argonne National Laboratory] A pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which is input.
PDB at a Glance
[National Institutes of Health] PDB At A Glance consists of a set of pre-defined biochemically meaningful search contexts (accessed by keyword) that represent the entire territory of the database.
[University College London] This service provides summaries and structural analyses of PDB data files.
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[Washington University, St. Louis] Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains based on the Swissprot 38 and SP-TrEMBL 11 protein sequence databases.
Pfam ftp Site
[Washington University, St. Louis] The ftp site for downloading the Pfam protein domain database and the associated tools.
PIR - International Protein Sequence Database
[Protein Information Resource] A database containing information concerning all naturally occurring wild-type proteins, of which the primary structure is known.
PRINTS BLAST Search
[University of Manchester] "This is an interface to a BLAST search of all protein sequences contained within the PRINTS database. The user entered sequence may be a protein or DNA sequence."
PRINTS: Protein Fingerprint Database
[University of Manchester] "PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used
to characterise a protein family; its diagnostic power is refined by iterative scanning of a
[Research Computing, Protein Information Resource] A non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
ProDom: The Protein Domain Database
[INRA] "The ProDom protein domain database consists of an automatic compilation of homologous domains."
[ExPASy] A searchable dictionary of proteins and patterns. Identifies to which family of proteins a sequence belongs.
Protein Data Bank
[Research Collaboratory for Structural Bioinformatics] The PDB is the single international repository for the processing and distribution of 3-D macromolecular
structure data primarily determined experimentally by X-ray crystallography and NMR. This is an indispensable resource for structural biology, especially proteins.
Protein Data Bank 3DB Browser
[PDB] Allows the user to rapidly search through the contents of the entire PDB Archive entries for obeying certain constraints.
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Protein Structure Database
[Pittsburgh Supercomputing Center] (PSdb) A new protein database that relates secondary (e.g. Helix, Sheet, Turn, Random Coil), supersecondary (e.g. helix-helix interactions), and tertiary information (e.g. Solvent accessibility, internal relative distances, and ligand interactions) to the primary structure. The data for each protein is supplied on a residue by residue basis and encoded in a series of flat ASCII files.
Protein Topology Home Page
[EBI] This site offers services devoted to protein structural topology and protein topology cartoons.
[Proteome, Inc.] This site allows access to proteome databases for yeast (YPD), S. pombe (PombePD), and C. elegans (WormPD). These databases contain genomic sequences, functional genomic, and other comprehensive organism information.
[Munich Information Center for Protein Sequences] ProtFam by MIPS is a curated protein classification database. In a joint effort, MIPS and
PIR-NBRF classify sequences into
superfamilies and families and annotate homology domains. This is part of the joint project to
produce the PIR-International Protein Sequence Database.
[Stanford University] "An exhaustive classification of all the proteins in the SWISSPROT and TrEMBL databases, into groups of related proteins. The analysis uses transitivity to identify homologous proteins, and within each group, every two members are either directly or transitively related."
[Institute for Pharmaceutical Chemistry, university of Marburg, Germany] Database system for analyzing receptor/ligand complexes deposited in the Protein Database.
Ribosomal Database Project II
[Center for Microbial Ecology] The Ribosomal Database Project (RDP) compiles ribosomal sequences and related data and redistributes them in aligned and phylogenetically ordered form. These sequences are drawn from various rRNA collections such as GenBank and from individual laboratories around the world. The database contains over 3000 aligned small subunit (SSU) and large subunit (LSU) ribosomal RNA sequences. Prokaryotic sequences predominate.
[ICGEBnet] A protein domain library with structural, functional, ligand-binding, and topogenic segments of proteins.
[ExPASy] Allows the user to browse through a number of databases, such as SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ENZYME, CD40Lbase, and SeqAnalRef; as well as other cross-referenced databases (EMBL/GenBank/DDBJ, OMIM, Medline, FlyBase, ProDom, SGD, and SubtiList). It also allows access to many analytical tools for the identification of proteins, the analysis of their sequences, and the prediction of their tertiary structures.
SCOP: Structural Classification of Proteins
[MRC Laboratory of Molecular Biology and Centre for Protein Engineering] Survey of known protein folds; information on close relatives of a given protein using keywords and homology searches.
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Search LITDB database using DBGET
[Protein Research Foundation] Search the literature of molecular aspects of proteins from about 1000 journals.
[ExPASy at the Swiss Institute of Bioinformatics] Data on proteins identified on various 2-D PAGE reference maps.
[ExPASy at the Swiss Institute of Bioinformatics] A database of high quality imagery of biological macromolecules with known three-dimensional structure.
SWISS-PROT and TrEMBL
[ExPASy] SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy, and high level of integration with other databases. TrEMBL is a computer-annotated supplement of SWISS-PROT that contains all the translations of EMBL nucleotide sequence entries not yet integrated in SWISS-PROT.
[DISC] Performs searches on sequences in protein and DNA databases for similarity to the query sequence, queries can include stop codons and IUPAC ambiguity codes.
TOPS: Protein Structural Topology
[European Bioinformatics Institute] This server allows searches of the TOPS database of topological patterns in protein structures.
[GBF] A database program that compiles data about gene regulatory DNA sequences; from this data programs have been developed to identify putative promoter or enhancer structures.
Uncharacterized Protein Families List
[ExPASy] (UPF) A list of uncharacterized protein families and an index of members. Information provided includes: name, origin, general information and a description.
The Yeast Genome
[Minich Information Center for Protein Sequences] Database for protein sequences, homology data and yeast genome information. Includes information on metabolic pathways.