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http://www.aspgd.org/

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

Proper citation: ASPGD (RRID:SCR_002047) Copy   

•   Source: SciCrunch Registry

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

The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): 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. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator

Proper citation: University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics (RRID:SCR_001921) Copy   

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http://www.proteinlounge.com

Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.

Proper citation: Protein Lounge (RRID:SCR_002117) Copy   

•   Source: SciCrunch Registry

http://microbes.ucsc.edu/cgi-bin/hgGateway?db=neisMeni_MC58_1

Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)

Proper citation: Neisseria meningitidis MC58 Genome Page (RRID:SCR_002200) Copy   

•   Source: SciCrunch Registry

http://bioafrica.mrc.ac.za/index.html

The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites.

Proper citation: BioAfrica HIV Informatics in Africa (RRID:SCR_002295) Copy   

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http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy   

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http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

Software to identify motifs, conserved regions, in DNA or protein sequences.

Proper citation: Gibbs Motif Sampler (RRID:SCR_002550) Copy   

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http://bioweb.ensam.inra.fr/esther

Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESTHER (RRID:SCR_002621) Copy   

•   Source: SciCrunch Registry

http://www.flymine.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

Proper citation: FlyMine (RRID:SCR_002694) Copy   

•   Source: SciCrunch Registry

https://ua.ilab.agilent.com/service_center/show_external/4535?name=analytical-and-biological-mass-spectrometry

Provides equipment and expertise for analysis of variety of biological and small molecules.Services include protein analysis encompassing protein identification, protein and peptide sequence confirmation, intact protein molecular weight determination, complex protein sample analysis, and protein/antibody drug interactions.Developed metabolomics library to support metabolomic and lipidomics analysis. Can identify range of post-translational modifications, determining their presence or absence, as well as quantitating PTMs.Proteomics and small molecule services include workflows for label free,chemical labeling (iTRAQ/TMT) and metabolic labeling (SILAC).Service for molecular synthesis, with monitoring reaction steps,calculating percentage of product, testing for purity, and molecule characterization with high resolution and high mass accuracy.Provides molecular weight and chemical composition determinations, structure elucidations and compound identification analysis or confirmation and accurate mass measurements of synthetic products, measurement of polymers, nucleic acids (DNA/RNA), peptides, proteins, natural products, and assistance with determination of unknowns.

Proper citation: University of Arizona Analytical and Biological Mass Spectrometry Core Facility (RRID:SCR_023370) Copy   

•   Source: SciCrunch Registry

http://chemistry.st-andrews.ac.uk/staff/jbom/group/databases.html

It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design.

Proper citation: Protein Ligand Database (RRID:SCR_006980) Copy   

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

Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword.

Proper citation: Dali database (RRID:SCR_006974) Copy   

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

Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly.

Proper citation: Consensus CDS (RRID:SCR_006729) Copy   

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

A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.

Proper citation: HIV-1 Human Protein Interaction Database (RRID:SCR_006879) Copy   

•   Source: SciCrunch Registry

https://myhits.sib.swiss/

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.

Proper citation: MyHits (RRID:SCR_006757) Copy   

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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://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   

•   Source: SciCrunch Registry

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