DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
|The Bioinformatics Educational Resource" info|
This site provides short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.
The 3D-GENOMICS database provides structural annotations for proteins from sequenced genomes.
|5S Ribosomal RNA|
5S ribosomal RNA is an integral component of the large subunit of all cytoplasmic and most organellar ribosomes. Its small size and association with ribosomal as well as non-ribosomal proteins made it an ideal model RNA molecule for studies of RNA structure and RNA-protein interactions.
|Amino Acid Indices And Similarity Matrices|
Database about physicochemical properties of amino acids.
|Aminoacyl-tRNA Synthetase Database" info|
Aminoacyl-tRNA synthetases (AARSs) are the key components of the protein biosynthesis machinery. They are responsible for maintaining the fidelity of transfer of genetic information from DNA into protein. The database is a compilation of amino acid sequences of all aminoacyl-tRNA synthetases known to date.
|Automatic Domain Decomposition Algorithm" info|
A Automatic Domain Decomposition Algorithm (ADDA) was used to generate a database of protein domain families with complete coverage of all protein sequences. Sequences are split into domains and domains are grouped into protein domain families in a completely automated process.
|Adipocyte Proteome Database" info|
Database of in-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics.
|Automatic Generated Test-Sets Database for Protein-Protein Docking|
Automatic Generated Test-Sets Database for Protein-Protein Docking (AGT-SDP) is a database providing test cases for protein-protein docking.
Database about genes, transcription and proteins from human and mouse.
|Antimicrobial Peptide Database|
Antimicrobial peptides exist widely from bacteria to mammals. They are encoded by the genome and produced through regular processes of gene transcription. They have an effect on bacteria, fungi, viruses, and even cancer cells. They can interact directly with biological membranes without requirement for specific receptors on the membranes.
ArchDB contains an automated classification of protein loop structure.
|Gene Regulation by Mammalian micro-RNAs|
MicroRNAs (miRNAs) constitute a class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis. By far the most important model systems in cancer research are mammalian organisms. Argonaute compiles comprehensive information on mammalian miRNAs, their origin and regulated target genes in an exhaustive database.
ArrayExpress is a public database of gene expression experiments. These experiments consist of multiple parts (or objects), in order to simplify querying we have provided a query interface which allows you to retrieve the most useful information relating to each experiment, the array(s) and the protocols(s) used.
|Active Sequences Collection|
ASC is a collection of active protein sequences, or protein fragments or subsequences, collected in the form of function-oriented databases.
|Artificial Selected Proteins / Peptides Database" info|
ASPD is a database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage display).
|Alternative Translational Initiation Database" info|
ATID is a database that provides a comprehensive collection of alternative translational initiation events. The purpose of this alternative translational initiation database (ATID) is to facilitate the systematic study of alternative translational initiation of genes.
|Xenopus laevis Database Focusing on Gene Expression" info|
Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The database was developed at the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg.
|Benchmark Alignment Database" info|
BAliBASE is a database for the comparison of multiple sequence alignments.
|Binding MOAD" info|
Binding MOAD is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding.
BMRB is a repository for data from NMR spectroscopy on proteins, peptides, and nucleic acids.
|Body Fluid Database|
Body fluids are one of the important targets for proteomics. Characterization of the protein composition of bodilyfluids could lead us to better understand human physiology. If a quantitative aspect is added, proteomics could contribute to the discovery of novel biomarkers.
BRAGI is an interactive protein modeling program. It was developed for the special
purpose to model unknown proteins from the structure of a known one. BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. One can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs. BRAGI includes also a set of programs and utility functions.
|Conformation Angles Database" info|
Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank.
|Protein Structure Classification" info|
CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).
|Consensus CDS (CCDS)|
The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality.
|Conserved Domain Database (CDD)" info|
Proteins often contain several modules or domains, each with a distinct evolutionary origin and function. The CD-Search service may be used to identify the conserved domains present in a protein sequence.
|3D Protein Structure Comparison and Alignment" info|
The CE-Database provides databases and tools for 3D protein structure comparison and alignment using the Combinatorial Extension (CE) Method.
CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.
|Clusters of Swiss-Prot and TrEMBL proteins|
The CluSTr database offers an automatic classification of UniProt Knowledgebase proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences.
coliBASE is a database for comparative genome analysis of E. coli.
|Bioinorganic Motif Database|
COME is an attempt to classify metalloproteins and some other complex proteins using the concept of bioinorganic motif.
|Chaperonin Database" info|
Type I chaperonins are molecular chaperones present in virtually all bacteria, some archaea and the plastids and mitochondria of eukaryotes. Sequences of cpn60 genes, encoding 60 kDa chaperonin protein subunits (CPN60, also known as GroEL or HSP60), are useful for phylogenetic studies and as targets for detection and identification of organisms.
|Cambridge Structural Database|
The world repository of small molecule crystal structures.
|Cold Shock Domain Database" info|
This is an interactive database which provides detailed information on proteins containing the so-called cold shock domain (CSD).
|DALI Domain Dictionary|
Dali stands for distance matrix alignment. The Dali server is an automatic service for the comparison of protein structure in 3D. You send the coordinates of a query structure and receive a multiple structure alignment in return. You can submit your coordinates either by electronic mail or interactively from the World Wide Web.
|Differentially Expressed Proteins in Human Cancer Database|
dbDEPC (database of Differentially Expressed Proteins in Human Cancer) is designed to store and display differentially expressed proteins (DEPs) in human cancers detected by mass spectrometry (MS) approach.
|Database of Protein Subcellular Localization|
DBSubLoc is a database of protein subcellular localization. This database contains proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
|Database of Copper-Chelating Proteins|
The Database of Copper-Chelating Proteins (DCCP) is maintained by Shandong Provincial Research Center for Bioinformatic Engineering and Technique. DCCP currently contains two types of proteins, one with 3D structure, called DCCP_3D, which contains 448 entries of proteins, and the other without 3D structure, called DCCP_1D, which contains 5088 entries.
|DExH/D Protein Family Database" info|
DExH/D proteins are essential for all aspects of cellular RNA metabolism and processing, in the replication of many viruses and in DNA replication. DExH/D proteins are subject to current biological, biochemical and biophysical research which provides a continuous wealth of data. The DExH/D protein family database compiles this information and makes it available over the WWW.
|Database of Interacting Proteins" info|
The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
|Database of Protein Disorder|
Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
|Database of Bacterial Lipoproteins" info|
Bacterial lipoproteins are a set of proteins modified at their N-terminal with N-Acyl Diacyl Glyceryl group (derived from phospholipids), which serves to anchor these proteins to carry out important functions efficiently at the membrane-aqueous interface.
|Database Of Ribosomal Crosslinks|
In order to interpret the molecular basis of the translational process, it is essential to have a corresponding knowledge of the higher structure of the ribosome. A large amount of biochemical data about structure of the ribosome is available at present. Ribosomal cross-linking is one of the most important methods which allows us to get such data.
|Disulphide Database" info|
DSDBASE is a database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
|Database of Simulated Molecular Motions" info|
The purpose of this database is to provide an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation. All of the movies are available through the internet.
|Macromolecular Structure Database" info|
The E-MSD macromolecular structure relational database is designed to be a single access point for protein and nucleic acid structures and related information.
|Electrostatic-Surface of Functional Site" info|
eFsite (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms.
|Edinburgh Mouse Atlas Project|
The Edinburgh Mouse Atlas consists of a digital atlas of mouse embryo development and spatially-mapped gene expression.
|Entrez Protein" info|
The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
|Endocrine Pancreas Consortium Database" info|
Genexpression database of the Endocrine Pancreas Consortium.
|Erythropoiesis Database" info|
The EpoDB (Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.
The database ist provided by the Computational Biology and Informatics Laboratory at the University of Pennsylvania.
|ESTerases and alpha / beta Hydrolase Enzymes and Relatives|
This server is dedicated to the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.
|Expert Protein Analysis System" info|
EXPASy (Expert Protein Analysis System) provides databases for the research on proteomics:
|ExPASy Proteomics Tools" info|
Tools for the analysis of the human proteom.
The EyeSite database is an information and modelling resource for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity.
|Fold classification based on Structure-Structure alignment of Proteins (FSSP)|
Fold classification - database on Structure-Structure alignment of proteins.
|Low-Complexity Peptides of Forming Amyloid Plaques|
Database about Peptides, which are capable of forming amyloid plaques.
|Functional Shift" info|
FunShift provides Functional shift analysis between the subfamilies of a Protein domain family.
|Genomic Distribution of Structural Superfamilies" info|
Genomic Distribution of Structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. The database has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases.
|Microarray Gene Annotation (GeneAnnot)" info|
Revised and improved annotation of Affymetrix human gene probe sets.
GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers:
GenePaint is a digital atlas of gene expression patterns in the mouse.
Genevestigator is one of the world's largest quality-controlled, curated and annotated databases of mouse Affymetrix arrays, and offers unique querying possibilities for molecular biologists.
|Gene Expression Omnibus" info|
The Gene Expression Omnibus is a high-throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval. GEO became operational in July 2000.
GermOnline is a database that provides access to microarray expression data from experiments relevant for the mitotic and meiotic cell cycle as well as gametogenesis in yeast and higher eukaryotes. In addition to that, GermOnline integrates knowledge about genes important for sexual reproduction.
|Gene Ontology Annotation (GOA)" info|
The Gene Ontology Annotation (GOA) database aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO).
|Endogenous GPCR List|
Information about what G protein coupled receptors are expressed in which cell lines.
|Information System for G Protein-Coupled Receptors (GPCRs)" info|
Information system about G protein-coupled receptors.
|Database of G-Proteins and their Interaction with GPCRs" info|
gpDB is a database of G-proteins and their interactions with GPCRs.
|Genomic Threading Database" info|
The Genomic Threading Database (GTD) contains structural annotations of proteomes, translated from the genomes of key organisms.
|Genomic Threading Database" info|
The Genomic Threading Database (GTD) contains structural annotations of proteomes, translated from the genomes of key organisms.
|Genomes To Protein Structures And Functions" info|
GTOP is a database built by the Laboratory of Gene-product Informatics at the National Institute of Genetics consisting of data analyses of proteins identified by various genome projects. This database mainly uses sequence homology analyses and features extensive utilization of information on three-dimensional structures. This research is supported by the Japan Science and Technology Corporation and Grants-in-Aid for Scientific Research (Genomes in category C) from the Ministry of Education, Science, Sports and Culture of Japan.
|Mouse Gene Expression Database|
Gene expression database from the mouse.
|Heart and Calcium Functional Network (HCNet) Database|
The Heart and Calcium functional Network (HCNet) database is a collection of functional gene modules calculated from the microarray data compendium available from the GEO database. It is a specialized database designed to assist experimentalists for cardiac calcium signaling research by providing the pre-calculated gene clusters and their potential correlation network in heart.
Hembase is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome.
|Hetero-Atoms in Protein Structures Database" info|
Proteins in Protein DataBank contains a lot of hetero atoms (Atoms that compose non-protein molecules). This information is useful to analyze protein-ligand/protein-substrate interactions. In Het-PDB Navi, information for hetero atoms is obtained through PDB ID and hetero atom name.
|Hetero-Compound Information Centre Uppsala" info|
HIC-Up is a server for hetero-compounds ("small molecules").
|Histone Sequence Database" info|
Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of non-histone proteins containing the histone fold motif exist. Novel histone and histone fold protein sequences continue to be added to public databases every year. The Histone Database is a searchable, periodically updated collection of histone fold-containing sequences derived from sequence-similarity searches of public databases.
|Database of Protein Domains and Motifs" info|
Hits is a database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently include regular expressions, generalized profiles and hidden Markov models.
|HIV-1 / Human Protein Interaction Database|
A database about the interaction of human immunodeficiency virus type 1 (HIV-1) proteins with those of the host cell, created by the National Institute of Allergy & Infectious Diseases.
Informations about Homeobox proteins, classification and evolution.
|Homeodomain Resource" info|
The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family.
HomoloGene is a system for automated detection of homologs among eukaryotic gene sets.
|Homologous Structure Alignment Database" info|
HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER.
|The Human Olfactory Receptor Data Exploratorium" info|
Olfactory receptors (ORs) constitute the largest multigene family in multicellular organisms. Their evolutionary proliferation has been driven by the need to provide recognition capacity for millions of potential odorants with arbitrary chemical configurations. Homo sapiens will likely be the first vertebrate species in which the complete OR repertoire will be known. You will find here information on the OR proteins, their structure, function and evolution. A set of analysis tools is provided.
|Homeobox Genes DataBase" info|
HOX-Pro is a database which arranges all available data on structure, function, phylogeny and evolution of Hox genes, Hox clusters and Hox networks.
|Human Proteomics Initiative" info|
The Human Proteomics Initiative is an initiative to annotate all human sequences.
|Human Plasma Membrane Receptome|
The human plasma membrane receptome is a protein sequences, literature, and expression database.
|Human Protein Reference Database" info|
The Human Protein Reference Database is a 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. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.
|Human Red Blood Cell Database|
hRBCD is a result of collaboration between the Department for Proteomics and Signal Transduction at the Max-Planck-Institut for Biochemistry and the Biomedical Primate Research Centre in the Netherlands.
|Homology-Derived Structures of Proteins (HSSP)" info|
HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein.
|Human Gene Expression Index (HuGE Index)" info|
Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
|Human Protein Atlas|
The protein atlas has been created to show the expression and localization of proteins in a large variety of normal human tissues and cancer cells. The data is presented as high resolution images representing immunohistochemically stained tissue sections. Available proteins (genes) can be reached through a specific search (by gene/protein name/id or classification, such as kinase or protease) or by browsing the individual chromosomes.
|Inter-Chain Beta-Sheets" info|
ICBS is a a database of protein-protein interactions mediated by interchain ß-sheet formation.
|Image Library of Biological Macromolecules" info|
The IMB Jena Image Library of Biological Macromolecules is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.
|IMGT/3Dstructure Database" info|
IMGT/3Dstructure-DB and IMGT/Structural-Query are a 3D structure database and a tool for immunological proteins. They are part of IMGT, the international ImMunoGenetics information system, a high-quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species, which consists of databases, Web resources and interactive on-line tools.
|The New England Biolabs Intein Database" info|
Inteins (protein splicing elements) database.
|Inner Ear Protein Database" info|
Database about the Proteom of the inner ear.
|IntAct Project" info|
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions.
|Database of Putative Protein Domain Interactions" info|
InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE).
|Interferon Stimulated Gene Database|
Database about genes induced by treatment with interferons.
The InterPro database is an integrated documentation resource for protein families, domains and functional sites.
|International Protein Index (IPI)" info|
The IPI (International Protein Index) provides a top level guide to the main databases that describe the human, mouse and rat proteomes: Swiss-Prot, TrEMBL, RefSeq and Ensembl.
IPI is created by identifying entries from the constituent databases that represent the same protein; and using these mappings to automatically create a datasets with maximum extent but minimum redundancy. For each protein in IPI, an entry from one of the constituent databases is selected as the master entry, and supplies the IPI entry with its sequence and annotation. Stable identifiers (with incremental versioning) are maintained to allow the tracking of sequences in IPI between IPI releases.
|Integrated Protein Knowledgebase" info|
The iProClass database provides value-added information reports for UniProtKB and unique UniParc proteins, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy. iProClass combines both data warehouse and hypertext navigation methods for integrating data, providing a comprehensive picture of protein properties that may lead to novel prediction and functional inference for previously uncharacterized "hypothetical" proteins and protein groups.
|Database of Chemical Compounds and Reactions in Biological Pathways" info|
KEGG LIGAND Database.
The universe of chemical reactions involving metabolites and other biochemical compounds, as well as xenobiotic compounds.
|Kidney Development Database|
The Kidney Development Database was created to collect in one place the data from a large number of developmental studies that have a bearing on the study of kidney development.
|Lipase Engineering Database" info|
The Lipase Engineering Database (LED) integrates information on sequence, structure, and function of lipases, esterases, and related proteins.
|Ligand-Gated Ion Channel Database" info|
Ligand-Gated Ion Channels are transmembrane proteins that can exist under different conformations, at least one forming a pore through the membrane connecting the two neighbour compartments.
|Database for Localization, Interaction, Functional assays and Expression of Proteins|
The Database for Localization, Interaction, Functional assays and Expression of Proteinsis created and maintained by Detlev Bannasch and Alexander Mehrle, DKFZ Heidelberg, Molecular Genome Analysis.
|LipOXygenases DataBase" info|
Due to their involvement in several diseases like cancer, inflammation, fever or arthritis, a lot of research is done on lipoxygenases yielding information about sequence, structure and function of these proteins. The LipOXygenases-DataBase (LOX-DB) is an effort to combine these informations and the related literature in one database and make it available via the internet.
MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution.
|MEROPS. The Protease Database.|
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The Summary page describing a given peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism. The Summary describes the classification and nomenclature of the peptidase and offers links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.
|DNA Methylation Database" info|
Database of DNA methylation.
|MOLecular INTeraction Database" info|
Database about molecular protein interactions.
|Major Intrinsic Proteins Database" info|
The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota.
|The MIPS Mammalian Protein-Protein Interaction Database" info|
The MIPS Mammalian Protein-Protein Interaction Database is produced by the
MIRAGE (Molecular Informatics Resource for the Analysis of Gene Expression) is a web site dedicated to methodologies, tools, and technologies relating to gene expression information. MIRAGE is a web resource of the Institute for Transcriptional Informatics (IFTI), Pittsburgh PA 15230-2556 USA.
|Mitochondrial Proteom Database" info|
Database about the mitochondrial proteom.
|Molecular Modeling Database" info|
NCBI's Entrez includes a database of experimentally determined three-dimensional biomolecular structures. Most 3D structure data are obtained from X-ray crystallography and NMR spectroscopy; they provide a wealth of information on biological function, on mechanisms linked to the function, and on the evolutionary history of and relationships between macromolecules.
|Comparative Protein Structure Models Database" info|
MODBASE is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure.
|Database of Macromolecular Movements" info|
The Database of Macromolecular Movements with Associated Tools for Geometric Analysis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis.
|Membrane Protein Data Bank" info|
Database about membrane-proteins.
|Nuclear Export Signals Database" info|
NESbase is a database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified.
|NetAffx Analysis Center" info|
NetAffx details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix.
|Nuclear Localization Signals (NLS) Database|
NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs, produced by Rajesh Nair & Phil Carter @ Rost Group, Columbia University, New York.
|Nuclear Matrix Associated Proteins - Database" info|
NMP-db is a database of nuclear matrix associated proteins, produced by Sven Mika @ Rost Group, Columbia University, New York.
|Nucleolar Proteome Database|
The Nucleolar Proteome Database contains all data from ongoing proteomic analysis of human nucleoli, which is carried out as a collaboration between the Lamond and Mann laboratories.
|Nuclear Protein Database" info|
The NPD contains information on >1000 vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Where appropriate, links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central).
|Nuclear Receptor Resource|
The Nuclear Receptor Resource (NRR) Project is a collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily.
|Information System for Nuclear Receptors" info|
Database about nuclear receptors.
|Nuclear Hormone Receptors Database" info|
NUREBASE is a reference database on Nuclear Hormone Receptors.
O-GlycBase is a database of glycoproteins with O-linked glycosylation sites.
|Olfactory Bulb Odor Map Database" info|
OdorMapDB is designed to be a database to support the experimental analysis of the molecular and functional organization of the olfactory bulb and its basis for the perception of smell.
|Cancer Microarray Database - Oncomine|
ONCOMINE collects all publicly available cancer microarray studies.
|Object-Oriented Transcription Factors Database" info|
ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database .
|Orientations of Proteins in Membranes (OPM) Database" info|
OPM provides hydrophobic thicknesses and orientations of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.
|Olfactory Receptor Database|
Olfactory receptors (ORs) are the largest family in the genome, and the first of a widening range of chemosensory receptors (CRs) in other chemosensory organs. ORDB began as a database of vertebrate OR genes and proteins and continues to support sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. Because of the associated growth of interest in other CRs, the database has grown over the years to include a broad range of chemosensory genes and proteins, that includes in addition to ORs the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), fungal pheromone receptors (FPRs) [these are informal abbreviations for tracking in ORDB, pending development of consensus nomenclature by the field].
|Organellar Map Database|
In the Organellar Map Database, a protein and peptide list with organellar map information is provided.
|OrthoDisease - A Database of Disease Gene Orthologs" info|
OrthoDisease is a database of model organism genes that are orthologous to human disease genes.
|Protein Alignments Organised as Structural Superfamilies DB" info|
PASS2 is a database of structural motifs of protein superfamilies.
|Protein Data Bank" info|
The data afford the 3-dimensional illustration of proteins.
The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan.
|Database of the Known 3D Structures of Proteins and Nucleic Acids|
PDBsum was created by Roman Laskowski of the European Bioinformatics Institute in Hinxton, U.K. This database provides synopses of structural and functional information stashed in the Protein Data Bank repository.
|Protein Databank of Transmembrane Proteins|
PDB_TM is a databank about transmembrane proteins.
|Protein-Protein Interaction Database for PDZ-Domains" info|
PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions.
|Predictions for Entire Proteomes" info|
PEP is a database of Predictions for Entire Proteomes, produced by the Rost Group, at Columbia University, New York.
|Peptide Conformation Database|
PepConf is a database of peptide conformations.
|Public Expression Profiling Resource (pepr)" info|
Public expression profiling resource provides expression profiles in a variety of diseases and conditions.
Peroxisomes are single-membrane subcellular organelles, present in most eukaryotic cells and organisms.
The Peroxisome fulfills essential metabolic functions in lipid metabolism, both catabolic (oxidation of pipecolic, phytanic and very-long chain fatty acids) and anabolic (synthesis of plasmalogens and bile acids). Moreover, the peroxisome plays a key role in free radical detoxification, differentiation, development and morphogenesis from human to yeast. Fatal disorders are related to defective peroxisomal function or biogenesis.
The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccaromyces cerevisiae (encoded by 61 genes).
|Protein Families Database of Alignments and HMMs|
Pfam is a collection of protein families and domains. Pfam contains multiple protein alignments and profile-HMMs of these families. Pfam is a semi-automatic protein family database, which aims to be comprehensive as well as accurate.
|Protein Folding Database" info|
The Protein Folding Database (PFD) is a collection of all biophysical data relating to experimental protein folding studies.
|Database of S/T/Y Phosphorylation Sites|
The Phospho.ELM database contains experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins. The entries, manually annotated and based on scientific literature, provide information about the phosphorylated proteins and the exact position of known phosphorylated instances.
|PhosphoBase - A Database of Phosphorylation Sites" info|
PhosphoBase contains information about phosphorylated residues in proteins and data about peptide phosphorylation by a variety of protein kinases.
|PIR International Protein Sequence Database|
The PIR, in collaboration with MIPS and JIPID, produces and distributes the PIR-International Protein Sequence Database (PSD), the most comprehensive and expertly annotated protein sequence database in the public domain. The primary objective for its continuing development and enhancement is to achieve the properties of: Comprehensiveness, Timeliness, Non-Redundancy, Quality Annotation, and Full Classification
|PIRSF SuperFamily Classification System" info|
The PIR superfamily/family concept, the original classification based on sequence similarity, has been used as a guiding principle to provide non-overlapping clusters of protein sequences to reflect their evolutionary relationships.
|Protein Mutant Database|
Compliations of protein mutant data are valuable as a basis for protein engineering. They provide information on what kinds of functional and/or structural influences are brought about by amino acid mutation at a specific position of protein.
|Proteome Profile Database" info|
PPD is a WWW-based database for comparative analysis of protein lengths in completely sequenced prokaryotic and eukaryotic genomes.
|Plasma Proteome Database|
PPD is a comprehensive list of blood proteins from Johns Hopkins University in Baltimore, Maryland, and the Institute of Bioinformatics in Bangalore, India. There is information about data from the literature on the more than 7500 protein variants that enter the plasma at some time. For each version, or isoform, one can find standard genomic information such as gene and amino acid sequences.
|HUPO - Plasma Proteom Project" info|
HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anti-coagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride).
|Predicted and Consensus Interaction Sites in Enzymes" info|
PRECISE (Predicted and Consensus Interaction Sites in Enzymes) is a database of interactions between the amino acid residues of an enzyme and its various ligands, i.e., substrate and transition state analogues, cofactors, inhibitors, and products.
PredictProtein is a service for sequence analysis, structure and function prediction. When submitting any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function.
|Protein Research Foundation - Literature Database" info|
The Peptide Institute, Protein Research Foundation, is collecting the information related to amino acids, peptides and proteins. All articles dealing with peptides from scientific journals accessible in Japan are collected.
|Amino Acids Sequence Database|
Japanese database about amino acids.
|PRoteomics IDEntifications Database" info|
The PRIDE PRoteomics IDEntifications database has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications.
|The PRINTS Fingerprint Database" info|
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 SWISS-PROT/TrEMBL composite.
ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
|Prokaryotic Lysis Enzymes Site|
ProLysES is a database of bacterial protease systems.
|The Prosthetic Groups and Metal Ions in Protein Active Sites Database|
Database about prosthetic groups and metal ions in protein active sites.
|Thermodynamic Database for Protein - Nucleic Acid Interactions" info|
ProNIT contains information about sequence, structure, bibliographic information and several thermodynamic parameters such as dissociation constant, association constant, changes in Gibbs free energy, enthalpy and heat capacity, activity (Km and kcat) etc., along with experimental method and conditions.
|PROSITE Database of Protein Families and Domains|
PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.
|Entrez Protein Database|
The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
|Proteome Analysis Database|
The Proteome Analysis database has been set up to provide comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms. The analysis is compiled using InterPro, CluSTr and GO Slim, and is performed on the non-redundant complete proteome sets of SWISS-PROT and TrEMBL entries.
ProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini.
|Thermodynamic Database for Proteins and Mutants|
ProTherm is a collection of numerical data of thermodynamic parameters such as Gibbs free energy change, enthalpy change, heat capacity change, transition temperature etc. for wild type and mutant proteins, that are important for understanding the structure and stability of proteins. It also contains information about secondary structure and accessibility of wild type residues, experimental conditions (pH, temperature, buffer, ion and protein concentration), measurements and methods used for each data, and activity information (Km and Kcat ).
This site offers an exhaustive classification of all the proteins in the SWISSPROT and TrEMBL databases, into groups of related proteins.
ProtoNet provides automatic hierarchical classification of protein sequences.
|Protein Reviews On The Web|
PROW Guides are authoritative short, structured reviews on proteins and protein families.
|Ribosomal Database Project|
The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.
|The Restriction Enzyme Database" info|
A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. REBASE was made by
Nobel laureate Dr. Richard J. Roberts and Dana Macelis.
|Database of the Translational Recoding Events (recode)" info|
The RECODE database is a compilation of translational recoding events (programmed ribosomal frameshifting, codon redefinition and translational bypass). The database provides information about the genes utilizing these events for their expression, recoding sites, stimulatory sequences and other relevant information.
|REFerence database for Gene EXpression Analysis" info|
Database for gene expression analysis.
|Database for Protein Renaturation" info|
Database of protocols describing the refolding and purification of recombinant proteins.
|Database for Comprehensive Analysis of Protein–Ligand Interactions|
The database behind Relibase is the Protein Data Bank (PDB). It covers all entries in the PDB which were determined experimentally by means of X-ray diffraction or NMR spectroscopy, but not theoretical structures.
TrEMBL is a computer-annotated protein sequence database supplementing the Swiss-Prot Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in Swiss-Prot. TrEMBL can be considered as a preliminary section of Swiss-Prot. For all TrEMBL entries which should finally be upgraded to the standard Swiss-Prot quality, Swiss-Prot accession numbers have been assigned. TrEMBL is split in two main sections: SpTrEMBL and RemTREMBL
The RESID Database is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link, pre-, co- and post-translational modifications.
|Ribosomal RNA Database|
This database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.
|Ribosomal Differentiation of Medical Microorganisms" info|
Database about the ribosomal differentiation of medical relevant microorganisms.
|Ribonuclease P Database" info|
The Ribonuclease P Database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information available electronically via the World Wide Web
|Ribosomal Protein Gene Database" info|
RPG is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms, including Drosophila melanogaster, Caenorhabditis elegans, Saccharo myces cerevisiae, Methanococcus jannaschii and Escherichia coli.
|Database of Receptor Tyrosine Kinase" info|
In this database, protein sequences from eight model metazoan species are organized under the format previously used for the HOVERGEN, HOBACGEN and NUREBASE systems.
|S/MAR Transaction DataBase" info|
S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold.
|Sarcomere Protein Gene Mutation Database|
Mutations in sarcomere protein genes are known to cause hypertrophic cardiomyopathy, dilated cardiomyopathy, and other diseases.
SBASE is a collection of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases (Vlahovicek et al, 2002). The protein domains are defined by their sequence boundaries given by the publishing authors or in one of the primary sequence databases (Swiss-Prot, PIR, TREMBL etc.). Domain groups are included if they have well defined sequence boundaries, and if they can be distinguished from other sequences using a similarity search technique.
|Structural Classification of Proteins" info|
The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships.
|SCOPe: Structural Classification of Proteins — extended" info|
SCOPe is a database developed at the Berkeley Lab and UC Berkeley that extends SCOP (version 1). SCOPe classifies many structures released since SCOP 1.75 through a combination of automation and manual curation, and corrects some errors, aiming to have the same accuracy as the fully hand-curated SCOP releases. SCOPe also incorporates and updates the Astral database.
|Database of Protein Catalytic Domains" info|
Database of protein catalytic domains.
|Structural Characterization Of Water, Ligands and Proteins" info|
SCOWLP (Structural Characterization Of Water, Ligands and Proteins) is a database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database includes proteins, peptidic-ligands and interface water molecules as descriptors of protein interfaces.
|Structural Database of Allergenic Proteins" info|
SDAP is a Web server that integrates a database of allergenic proteins with various bioinformatics tools for performing structural studies related to allergens and characterization of their epitopes.
|7 Transmembrane Helix Receptor Database (7-TMR)|
SEVENS is a database including 7-TMR (7 transmembrane helix receptor) candidates predicted from whole human genome sequences, using sequence search, motif and domain assignment, transmembrane helix prediction and the gene quality refinement.
|Simple Modular Architecture Research Tool" info|
SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins.
|Stanford Microarray Database" info|
SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
|Stanley Medical Research Institute Online Genomics Database" info|
The Stanley Medical Research Institute online genomics database (SMRIDB) is a web-based system for understanding the genetic effects of human brain disease (i.e. bipolar, schizophrenia, and depression). This database contains fully annotated clinical metadata and gene expression patterns.
|Secreted Protein Database|
Database about proteins which are secreted outside of the cell membrane.
|Signal Peptide Database" info|
SPdb is a signal peptide database containing signal/leader sequences of archaea, prokaryotes and eukaryotes.
|Signal Recognition Particle Database" info|
SRPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically Ordered sequences related to structure and function of SRP.
|Structure Superposition Database (SSD)" info|
The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function.
|Super LIgands" info|
Super Ligands contains small molecule structures occurring as ligands in the Protein Data Bank.
|HMM Library and Genome Assignments Server" info|
The SUPERFAMILY database provides structural assignments to protein sequences and a framework for analysis of the results.
|SUrface Residues and Functions Annotated, Compared and Evaluated" info|
The SURFACE database is a repository of annotated and compared protein surface regions.
SPTR (accessible as SWall on the EBI SRS server) is a comprehensive protein sequence database that combines the high quality of annotation in Swiss-Prot with the completeness of the weekly updated translation of all protein coding sequences from the EMBL nucleotide sequence database.
|Sweden Peptide Database" info|
SwePep is an endogenous peptide database developed by the Laboratory for Biological and Medical Mass Spectrometry at Uppsala University to aid mass spectrometric identifications.
|Swiss Prot Protein Knowledgebase|
Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
|Two-dimensional Polyacrylamide Gel Electrophoresis Database|
SWISS-2DPAGE contains data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.
|SWISS-MODEL Repository" info|
The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. The repository is developed at the Biozentrum Basel within the Swiss Institute of Bioinformatics.
This Database contains information on:
|SYSTEmatic Re-Searching (systers)" info|
SYSTERS is a collection of graph-based algorithms to hierarchically partition a large set of protein sequences into homologous families and superfamilies. The methods unified now under the name SYSTERS (short for SYSTEmatic Re-Searching) are based on an all-against-all database search (using Smith-Waterman comparisons on a GeneMatcher machine).
|Target Search for Structural Genomics" info|
TargetDB is a target registration database funded by the NIH that was developed to provide registration and tracking information for the NIH P50 structural genomics centers.
|Transcription Element Listening System (TELiS)" info|
TELiS combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.
TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFAM, the full alignment of all family members and the cutoff scores for inclusion in each of the TIGRFAMs.
|Tissue-Specific Promoter Database|
TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve sets of promoters according to their tissue-specific activity or according to individual Gene Ontology terms the corresponding genes are assigned to.
|Gene Expression in Tooth|
Database about the geneexpression in tooth.
|Topology of Protein Structures Database" info|
The TOPS database holds topological descriptions of protein structures.
UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
|Virus Database at University College London" info|
VIDA is a virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses.
|Virus Particle Explorer (viper)" info|
VIPER is a Website for virus capsid structures and their computational analyses.
|Voltage-gated Potassium Channel Database" info|
Voltage-gated potassium channel database (VKCDB) is designed to serve as a resource for research on voltage-gated potassium channels. Protein sequences, references, functional data and many other relevant data are included in this database.
|WebQTL Project" info|
WebQTL stors data about gene expression, neuropharmacological,anatomical, and behavioral data for over 30 strains of mice.
|The Wnt gene Homepage|
Wnt proteins form a family of highly conserved secreted signaling molecules that regulate cell-to-cell interactions during embryogenesis. Wnt genes and Wnt signaling are also implicated in cancer. Insights into the mechanisms of Wnt action have emerged from several systems: genetics in Drosophila and Caenorhabditis elegans; biochemistry in cell culture and ectopic gene expression in Xenopus embryos. Many Wnt genes in the mouse have been mutated, leading to very specific developmental defects.
|YEAST Protein Complex Database" info|
This website contains the information on protein-protein interactions and protein complex worked out by a group of scientists at Cellzome AG and the European Molecular Biology Laboratory in Heidelberg, Germany.