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http://rkd.ucdavis.edu/interactome.shtml

It was created to host functional genomic information gathered as part of a large NSF funded rice kinase proteomics project. The goal is to integrate disparate data sets into a logical, user friendly format. To accomplish this, they have developed a platform to display user selected functional genomic data on a phylogenetic tree. The RKD also includes an interactive chromosomal map showing the positions of all rice kinases and an interactive protein-protein interaction maps.

Proper citation: Rice Kinase Database (RRID:SCR_006990) Copy   

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http://bioinformatics.biol.uoa.gr/cuticleDB

A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.

Proper citation: CuticleDB (RRID:SCR_007045) Copy   

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http://www.signaling-gateway.org/molecule/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Relational database of all significant published qualitative and quantitative information on cell signaling proteins. The Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. The goal is to filter the data to present only validated information. In addition, the Gateway is the home of Signaling Update, which provides a one-stop overview of the latest and hottest research in cell signaling for both the specialist and non-specialist alike.

Proper citation: UCSD-Nature Signaling Gateway Molecule Pages (RRID:SCR_006907) Copy   

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http://tardis.nibio.go.jp/homstrad/

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. These structure-based alignments are annotated with JOY and examined individually.

Proper citation: HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) Copy   

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http://www.wwpdb.org/

Public global Protein Data Bank archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by individual member organizations and about projects undertaken by wwPDB. Data available via websites of its member organizations.

Proper citation: Worldwide Protein Data Bank (wwPDB) (RRID:SCR_006555) Copy   

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http://gbrowse.org/

A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions.

Proper citation: GBrowse (RRID:SCR_006829) Copy   

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 04, 2014. Curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, etc). The database also contains modules for pairwise correlation analysis and BLAST search.

Proper citation: Artificial Selected Proteins/Peptides Database (RRID:SCR_007557) Copy   

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http://bond.unleashedinformatics.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus.

Proper citation: Biomolecular Object Network Databank (RRID:SCR_007433) Copy   

•   Source: SciCrunch Registry

http://www.eurasnet.info/tools/asdatabases

It has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns. Version 2.1 of ASDB consists of two divisions, ASDB(proteins) , which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences.
SWISS-PROT uses two formats for description of alternative splicing Thus the protein sequences were selected from SWISS-PROT using full text search for both the words alternative splicing (usually in the CC lines) and varsplic (in the FT lines). In order to group proteins that could arise by alternative splicing of the same gene, we developed the clustering procedure. Two proteins were linked if they had a common fragment of at least 20 amino acids, and clusters were initially defined as maximum connected groups of linked proteins. It turned out that some clusters were chimeric, in the sense that they contained members of multi-gene families, but not alternatively spliced variants of one gene. Therefore the multiple alignments were subject to additional analysis aimed at detection of chimeric clusters.
Each cluster is represented by multiple alignment of its members constructed using CLUSTALW. The distribution of cluster size, representation of species and other relevant statistics of ASDB(proteins) can be accessed through the links below.
This processing covers the cases when alternatively spliced variants are described in separate SWISS-PROT entries. The other kinds of ASDB records, originating from the SWISS-PROT entries with the varsplic field in the feature table, usually describe the proteins that are not part of any cluster. In these cases, the information on the variable fragments of the several proteins which result from the alternative splicing of a single gene is contained in the entry itself. ASDB(proteins) entries are marked with different symbols to allow for easy differentiation among the three types: those proteins which are part of the ASDB clusters and the corresponding multialignments, those which have the information on different variants in the associated SWISS-PROT entries, and those for which the information on the variants is not available at the present time. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SWISS-PROT entries.
The ASDB(nucleotides) division was generated by collecting all GenBank entries containing the words alternative splicing and further selection of those entries that contain complete gene sequences (all CDS fields are complete, i.e. they do not have continuation signs).
Sponsors: This work was supported by the Director, Office of Energy Research, Office of Biological and Environmental Research, of the US Department of Energy under Contract No. DE-ACO3-76SF00098. Additional support came from grants from the Russian Fund of Basic Research (99-04-48347), the Russian State Scientific Program Human Genome (65/99), and the Merck Genome Research Institute (244).

Proper citation: Alternative Splicing Database (RRID:SCR_007555) Copy   

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http://mips.gsf.de/genre/proj/ustilago/

The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.

Proper citation: MIPS Ustilago maydis Database (RRID:SCR_007563) Copy   

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http://www.dddc.ac.cn/pdtd/

It is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Drug targets of PDTD were categorized into 15 and 13 types according to two criteria: therapeutic areas and biochemical criteria. The database supports extensive searching function using PDB ID, target name and category, related disease.

Proper citation: Potential Drug Target Database (RRID:SCR_007069) Copy   

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http://source.rcsb.org/jfatcatserver/ceHome.jsp

CE is a databases of alignments for all polypeptide chains. A representative set of proteins is available and kept current with the PDB, a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment. Complete details are described in the paper (PDF format). Databases of alignments for all polypeptide chains and a representative set of proteins is available and kept current with the PDB

Proper citation: Combinatorial Extension (CE) (RRID:SCR_007585) Copy   

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http://www.ncbi.nlm.nih.gov/COG

A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.

Proper citation: COG (RRID:SCR_007139) Copy   

•   Source: SciCrunch Registry

http://www.disprot.org/

The 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. Users can BLAST sequences, browse by protein name, or view by protein function and functional subclass.

Proper citation: DisProt - Database of Protein Disorder (RRID:SCR_007097) Copy   

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http://caps.ncbs.res.in/gendis/home.html

Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. GenDiS has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases. Sequences showing reliable homology to entries in SCOP and PASS2 databases have been obtained from the non-redundant protein sequence database and aligned. Similar alignments of the superfamily members are provided in the genome level. GenDiS provides a platform for cross genome comparison at the superfamily level. GenDis relates proteins sequence information across all strata of taxonomy. One may navigate through the database to obtain structural homologues across different levels in taxonomic classification. The nomenclature of the various genomes and their hierarchy is in direct correspondence with the taxonomy database maintained at the NCBI. Sequence homologues for the various structural members are obtained from the non-redundant protein sequence database employing sensitive sequence search methods. Multiple approaches such as PSI-BLAST, HMMsearch of the HMMer suite and an interacting motif constrained PHI-BLAST have been employed to identify homologues in the sequence databases.

Proper citation: Genomic Distribution of structural Superfamilies (RRID:SCR_007670) Copy   

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http://genolist.pasteur.fr/Colibri/

Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Colibri (RRID:SCR_007606) Copy   

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http://ppa.bcf.ku.edu/DB_PABP/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. DB-PABP is an attempt to document the publicly available experimentally determined polyanion binding proteins (PABPs). The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies. The database is manually curated. It uses protein annotations from NCBI protein database and literature information is retrieved from PubMed. Whenever applicable, links to NCBI protein database and PubMed are provided so users may access additional information available in these public databases.

Proper citation: DB-PABP: a database of polyanion binding proteins (RRID:SCR_007603) Copy   

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http://dbptm.mbc.nctu.edu.tw/

dbPTM is a database that compiles information on protein post-translational modifications (PTM) such as the modified sites, solvent accessibility of surrounding amino acids, protein secondary and tertiary structures, protein domains, and protein variations. The version 2.0 of dbPTM integrates the experimentally validated PTM sites with referable literatures from Swiss-Prot, Phospho.ELM, O-GLYCBASE, and UbiProt. In all of the collected PTM information, about 25 types of PTM with enough experimentally validated sites are trained the profile hidden Markov models (HMMs) to detect the potential PTM sites with 100% specificity against Swiss-Prot proteins. To help users investigating more detail in each type of PTM, the substrate peptide specificity such as positional amino acid frequency, solvent accessibility and secondary structure surrounding the modified sites are also provided. Moreover, the information of orthologous protein clusters is provided to users for analyzing whether the PTM sites located in the evolutionary conserved regions or not., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dbPTM: An informational repository of proteins and post-translational modifications (RRID:SCR_007619) Copy   

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http://firedb.bioinfo.cnio.es/

A database of Protein Data Bank structures, ligands and annotated functional site residues. The database can be accessed by PDB codes or UniProt accession numbers as well as keywords. FireDB contains information on every chemical compound in the PDB, including their descriptions, the PDB structures in which the compounds are found and the amino acids that are in contact with the ligand.

Proper citation: FireDB (RRID:SCR_007655) Copy   

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http://cgl.imim.es/fcp/

FCP is a publicly accessible web tool dedicated to analyzing the current state and trends of available proteome structures along the classification schemes of enzymes and nuclear receptors. It offers both graphical and quantitative data on the degree of functional coverage in that portion of the proteome by existing structures and on the bias observed in the distribution of those structures among proteins. Users can choose to search the website based on structures or ligands, and can also sort by enzyme or receptor. Users can also view data based on structural and population (species) filters.

Proper citation: Functional Coverage of the Proteome (RRID:SCR_007654) Copy   

•   Source: SciCrunch Registry