DATABASES ON MEDICINE AND MOLECULAR BIOLOGY
[German]  [Feedback]

 

HOTLINKS >>> GENBANK EBI NCBI MEDLINE
Amino Acid Indices And Similarity Matrices
 

Database about physicochemical properties of amino acids.
http://www.genome.ad.jp/aaindex/

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.
http://rose.man.poznan.pl/aars/index.html

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.
The current database contains domains for more than 1.5 million sequences in more than 40,000 domain families. In particular, there are 3828 novel domain families that do not overlap with the curated domain databases Pfam, SCOP and InterPro.
http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

Adipocyte Proteome Database"  info
 

Database of in-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics.
http://141.61.102.16/adipo/

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.
http://bibiserv.techfak.uni-bielefeld.de/agt-sdp/

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.
http://aps.unmc.edu/AP/main.php

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).
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/

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.
http://bioinfo.au.tsinghua.edu.cn/atie/

Binding MOAD"  info
 

Binding MOAD is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding.
http://www.BindingMOAD.org

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.
http://www.mapuproteome.com/

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.
http://www.ncbi.nlm.nih.gov/projects/CCDS/

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.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

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.
http://www.ebi.ac.uk/clustr/

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.
http://www.cpndb.ca/

Cold Shock Domain Database"  info
 

This is an interactive database which provides detailed information on proteins containing the so-called cold shock domain (CSD).
http://www.chemie.uni-marburg.de/~csdbase/welcome.html

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.
http://ekhidna.biocenter.helsinki.fi/dali/start

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.
http://protchem.hunnu.edu.cn/depd/

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.
http://sdbi.sdut.edu.cn/DCCP/en/index.php

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.
http://www.dexhd.org/

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.
http://dip.doe-mbi.ucla.edu

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.
http://www.mrc-lmb.cam.ac.uk/genomes/dolop/

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.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

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.
http://bioweb.ensam.inra.fr/ESTHER/general?what=index

Database for Proteins with an Experimentally Verified Function"  info
 

EXProt is a non-redundant database containing protein sequences for which the function has been experimentally verified.
http://www.cmbi.kun.nl/EXProt/

"  info
 

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.
A principal feature of the site is structural annotations,which range from experimentally solved structures to close structural neighbours to distant structure predictions. Many pre-generated homology models are provided.
http://eyesite.cryst.bbk.ac.uk/

Fold classification based on Structure-Structure alignment of Proteins (FSSP)
 

Fold classification - database on Structure-Structure alignment of proteins.
http://www.ebi.ac.uk/Databases/structure.html

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.
http://FunShift.cgb.ki.se/

Endogenous GPCR List
 

Information about what G protein coupled receptors are expressed in which cell lines.
http://www.tumor-gene.org/GPCR/gpcr.html

Information System for G Protein-Coupled Receptors (GPCRs)"  info
 

Information system about G protein-coupled receptors.
http://www.gpcr.org/7tm/

Database of G-Proteins and their Interaction with GPCRs"  info
 

gpDB is a database of G-proteins and their interactions with GPCRs.
http://bioinformatics2.biol.uoa.gr/gpDB/index.jsp

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.

http://research.nhgri.nih.gov/histones/

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.
http://hits.isb-sib.ch/

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.
http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/

Homeobox Page
 

Informations about Homeobox proteins, classification and evolution.
http://www.biosci.ki.se/groups/tbu/homeo.html

Homeodomain Resource"  info
 

The Homeodomain Resource is a searchable, curated collection of information for the homeodomain protein family.
http://research.nhgri.nih.gov/homeodomain/

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.
http://bip.weizmann.ac.il/HORDE/

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.
http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html

Human Proteomics Initiative"  info
 

The Human Proteomics Initiative is an initiative to annotate all human sequences.
http://www.ebi.ac.uk/swissprot/hpi/hpi.html

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.
HPRD is made by PandeyLab and the Institute of Bioinformatics.
http://www.hprd.org/

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.
http://141.61.102.16/rbc/

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.
http://www.proteinatlas.org/

Inter-Chain Beta-Sheets"  info
 

ICBS is a a database of protein-protein interactions mediated by interchain ß-sheet formation.
http://www.igb.uci.edu/servers/icbs/

The New England Biolabs Intein Database"  info
 

Inteins (protein splicing elements) database.
http://www.neb.com/neb/inteins.html

Inner Ear Protein Database"  info
 

Database about the Proteom of the inner ear.
http://oto.wustl.edu/thc/innerear2d.htm

IntAct Project"  info
 

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions.
http://www.ebi.ac.uk/intact/

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).
http://interdom.i2r.a-star.edu.sg/

InterPro
 

The InterPro database is an integrated documentation resource for protein families, domains and functional sites.
http://www.ebi.ac.uk/interpro/index.html

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.
http://www.ebi.ac.uk/IPI/IPIhelp.html

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.
http://pir.georgetown.edu/iproclass/

Lipase Engineering Database"  info
 

The Lipase Engineering Database (LED) integrates information on sequence, structure, and function of lipases, esterases, and related proteins.
http://www.led.uni-stuttgart.de/

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.
In the LGIC Database one will find the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided.
http://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php

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.
http://www.dkfz.de/LIFEdb/

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.
This database ist maintained by the DKFZ (Deutsches Krebsforschungszentrum) in Heidelberg.
http://www.glycosciences.de/spec/lox-db/

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.
http://merops.sanger.ac.uk/

MOLecular INTeraction Database"  info
 

Database about molecular protein interactions.
http://mint.bio.uniroma2.it/mint/

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.
http://idefix.univ-rennes1.fr:8080/Prot/index.html

The MIPS Mammalian Protein-Protein Interaction Database"  info
 

The MIPS Mammalian Protein-Protein Interaction Database is produced by the Munich Information Center for Protein Sequences.
http://mips.gsf.de/proj/ppi/

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.
http://www.cbs.dtu.dk/databases/NESbase/

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.
http://cubic.bioc.columbia.edu/db/NLSdb/

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.
http://www.rostlab.org/services/NMPdb/

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.
http://www.lamondlab.com/NOPdb/

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).
http://npd.hgu.mrc.ac.uk/

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.
http://nrresource.org/

Information System for Nuclear Receptors"  info
 

Database about nuclear receptors.
http://www.receptors.org/NR/

Nuclear Hormone Receptors Database"  info
 

NUREBASE is a reference database on Nuclear Hormone Receptors.
Nuclear hormone receptors are a very important class of ligand-activated transcription factors, found in varying numbers in all animals. The receptors play essential roles in embryonic development, maintenance of differentiated cellular phenotypes, metabolism and cell death. Malfunction or deregulation of the receptors leads to proliferative, reproductive, and metabolic diseases such as cancer, infertility, obesity and diabetes.
http://nurexbase.prabi.fr/

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.
http://senselab.med.yale.edu/odormapdb/

Object-Oriented Transcription Factors Database"  info
 

ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database .
http://www.ifti.org/ootfd/

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].
http://senselab.med.yale.edu/senselab/ordb/

Organellar Map Database
 

In the Organellar Map Database, a protein and peptide list with organellar map information is provided.
http://141.61.102.16/ormd/

Protein Data Bank"  info
 

The data afford the 3-dimensional illustration of proteins.
http://www.rcsb.org/pdb/

PDBbind
 

The PDBbind database is developed in Dr. Shaomeng Wang's group at the University of Michigan.
The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). All of the binding affinity data compiled in the PDBbind database were collected from original references.
http://www.pdbbind.org/

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.
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/

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.
http://icb.med.cornell.edu/services/pdz/start

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
http://pir.georgetown.edu/pirwww/search/textpsd.shtml

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.
http://pir.georgetown.edu/pirsf/

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.
The Protein Mutant Database (PMD) covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants.
http://pmd.ddbj.nig.ac.jp/

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.
http://www.plasmaproteomedatabase.org/

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).
http://www.bioinformatics.med.umich.edu/hupo/ppp

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.
http://precise.bu.edu/precisedb/

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.
http://www.prf.or.jp/litdb.html

Amino Acids Sequence Database
 

Japanese database about amino acids.
http://www.prf.or.jp/en/litq.html

Protein Interaction and Molecular Information Database
 

PRIME is a develped version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface.
http://prime.ontology.ims.u-tokyo.ac.jp:8081/

ProDom"  info
 

ProDom is a comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
http://prodom.prabi.fr/prodom/current/html/home.php

Prokaryotic Lysis Enzymes Site
 

ProLysES is a database of bacterial protease systems.
http://genome.ukm.my/prolyses/

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.
http://gibk26.bio.kyutech.ac.jp/jouhou/pronit/pronit.html

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.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein

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 ).
http://gibk26.bio.kyutech.ac.jp/jouhou/Protherm/protherm.html

ProtoMap"  info
 

This site offers an exhaustive classification of all the proteins in the SWISSPROT and TrEMBL databases, into groups of related proteins.
http://protomap.stanford.edu/

ProtoNet"  info
 

ProtoNet provides automatic hierarchical classification of protein sequences.
http://www.protonet.cs.huji.ac.il/

Protein Reviews On The Web
 

PROW Guides are authoritative short, structured reviews on proteins and protein families.
The Guides provide approximately 20 standardized categories of information (abstract, biochemical function, ligands, references, etc.) for each protein.
http://www.ncbi.nlm.nih.gov/prow/

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.
http://rebase.neb.com/

Database for Protein Renaturation"  info
 

Database of protocols describing the refolding and purification of recombinant proteins.
http://refold.med.monash.edu.au/

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.
http://relibase.ccdc.cam.ac.uk/

Remaining TrEMBL
 

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
RemTrEMBL (Remaining TrEMBL) contains the entries that we do not want to include in Swiss-Prot.

  • Immunoglobulins and T-cell receptors
  • Synthetic sequences
  • Patent application sequences
  • Small fragments
  • CDS not coding for real proteins
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbNl1KbLfG+-lib+REMTREMBL

  • RESID"  info
     

    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.
    http://pir.georgetown.edu/cgi-bin/resid

    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
    http://www.mbio.ncsu.edu/RNaseP/

    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.
    http://pbil.univ-lyon1.fr/RTKdb/

    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.
    http://smartdb.bioinf.med.uni-goettingen.de/

    Sarcomere Protein Gene Mutation Database
     

    Mutations in sarcomere protein genes are known to cause hypertrophic cardiomyopathy, dilated cardiomyopathy, and other diseases.
    http://genetics.med.harvard.edu/~seidman/cg3/index.html

    Sbase"  info
     

    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.
    http://hydra.icgeb.trieste.it/sbase/

    Database of Protein Catalytic Domains"  info
     

    Database of protein catalytic domains.
    http://www.enzome.com/

    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.
    http://www.scowlp.org

    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.
    http://fermi.utmb.edu/SDAP/

    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.
    http://smart.embl-heidelberg.de/

    Secreted Protein Database
     

    Database about proteins which are secreted outside of the cell membrane.
    http://spd.cbi.pku.edu.cn/

    Signal Peptide Database"  info
     

    SPdb is a signal peptide database containing signal/leader sequences of archaea, prokaryotes and eukaryotes.
    http://proline.bic.nus.edu.sg/spdb/

    Signal Recognition Particle Database"  info
     

    SRPDB (Signal Recognition Particle Database) provides aligned, annotated and phylogenetically Ordered sequences related to structure and function of SRP.
    http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html

    Super LIgands"  info
     

    Super Ligands contains small molecule structures occurring as ligands in the Protein Data Bank.
    http://bioinf.charite.de/superligands/

    SWALL
     

    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.
    http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-page+LibInfo+-id+1rbNl1KbLbm+-lib+SWALL

    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.
    http://www.swepep.org/

    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.
    http://us.expasy.org/sprot/

    SYFPEITHI"  info
     

    This Database contains information on:

  • Peptide sequences
  • anchor positions
  • MHC specificity
  • source proteins, source organisms
  • publication references
    http://www.syfpeithi.de/

  • 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).
    http://systers.molgen.mpg.de/

    TIGRFAMs"  info
     

    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.
    http://www.jcvi.org/

    UniProt"  info
     

    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.
    UniProt is comprised of three components, each optimized for different uses. The UniProt Knowledgebase (UniProt) is the central access point for extensive curated protein information, including function, classification, and cross-reference. The UniProt Non-redundant Reference (UniRef) databases combine closely related sequences into a single record to speed searches. The UniProt Archive (UniParc) is a comprehensive repository, reflecting the history of all protein sequences.
    http://www.uniprot.org/

    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.
    http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html

    Virus Particle Explorer (viper)"  info
     

    VIPER is a Website for virus capsid structures and their computational analyses.
    http://viperdb.scripps.edu/

    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.
    http://vkcdb.biology.ualberta.ca

    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.
    http://www.stanford.edu/group/nusselab/cgi-bin/wnt/

    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.
    http://yeast-complexes.embl.de/