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https://www.oxfordjournals.org/our_journals/nar/database/summary/954

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A database for the study of protein inter-atomic distance distribution. Currently, the distances are extracted from the protein structures determined through X-ray Crystallography, but they could also be obtained from NMR structural models. The known structures with the resolution higher than 2A and less than 70% sequence similarities are selected. Each type of distances is specified in terms of the types of the atoms it involves, the types of the residues containing the atoms, and the types of the residues in between the two end residues in sequence. An automated system is built to generate and process the data dynamically. The system consists of two levels of databases. The first one stores the sequence and structure information for a large set of high-resolution protein structures, with a similar data structure as the structural data represented in the PDB Data Bank. The second one stores the information for the distance distributions, with each record corresponding to a distribution function. The second database is built dynamically from the first one. The database can provide structural information in terms of distance distributions to structural biologists. Such information can be valuable for the study of many fundamental biological problems including protein structure prediction and determination, protein dynamics simulation, molecular design, protein structural analysis and classification, etc.

Proper citation: PIDD (RRID:SCR_007854) Copy   

•   Source: SciCrunch Registry

http://www.bioinfodatabase.com/pint/

A protein-protein interactions thermodynamic database which contains data of several thermodynamic parameters along with sequence and structural information experimental conditions and literature information. Each entry contains numerical data for features of the interacting proteins such as the free energy change, dissociation constant, association constant, enthalpy change, and heat capacity change. PINT includes: the name and source of the proteins involved in binding, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, and experimental conditions such as buffers, ions and additives, and literature information. PINT is cross-linked with other related databases such as PIR, SWISS-PROT, PDB and the NCBI PUBMED literature database.

Proper citation: PINT (RRID:SCR_007856) Copy   

•   Source: SciCrunch Registry

http://www.p3db.org

It was established with an overall objective to provide a resource of protein phosphorylation data from multiple plants. P3DB was constructed with a dataset from oilseed rape. The data was obtained using a combination of data-dependent neutral loss and multistage activation mass spectrometry. The dataset includes 14,670 non-redundant phosphorylation sites from 8,894 phospho-peptides in 6,382 substrate proteins.

Proper citation: Plant Protein Phosphorylation Database (RRID:SCR_007841) Copy   

•   Source: SciCrunch Registry

http://www.orenza.u-psud.fr/

ORENZA is a relational database of Orphan Enzyme Activities. ORENZA provides an accurate and up to date list of Enzyme Activities for which no sequences are available in the main sequence protein databases. Orphan enzyme activities correpond to the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), and which are not associated with any amino acid sequences in the major public databases.

Proper citation: ORENZA : a database of ORphan ENZyme Activities (RRID:SCR_007836) Copy   

•   Source: SciCrunch Registry

http://www.iris.irri.org

IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data.

Proper citation: IRIS - International Rice Information System (RRID:SCR_007755) Copy   

•   Source: SciCrunch Registry

http://pir.georgetown.edu/iprolink

iProLINK (integrated Protein Literature, INformation and Knowledge) has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development. The collection of data sources can be utilized by computational and biological researchers to explore literature information on proteins and their features or properties. The data sources for bibliography mapping and feature evidence attribution include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database.

Proper citation: iProLINK (RRID:SCR_007752) Copy   

•   Source: SciCrunch Registry

http://line1.molgen.mpg.de

L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database.

Proper citation: L1Base (RRID:SCR_007750) Copy   

•   Source: SciCrunch Registry

http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. It includes: Tracks Display- View splicing diagrams for any gene in the Sanger C. elegans database alongside cDNA and EST alignments. Retrieve DNA sequences with the exons in upper case. Search the literature. Alt Splicing Catalog - As defined by Chuck's altGraphX process. A frames based viewer linking to the genome browser. Alt-Splicing Catalog - A catalog of genes for which the cDNA and EST evidence indicates alternative splicing.

Proper citation: The Intronerator (RRID:SCR_007745) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ipd/hpa/

A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003.

Proper citation: IPD-HPA - Human Platelet Antigens (RRID:SCR_007747) Copy   

•   Source: SciCrunch Registry

http://www.plprot.ethz.ch/

A plastid protein database. It integrates data from large scale proteome analyses of different plastid types.These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison allows establishing a core proteome that is common to all plastid types and provides furthermore information about plastid type-specific functions.

Proper citation: PLprot (RRID:SCR_007864) Copy   

•   Source: SciCrunch Registry

http://pirnabank.ibab.ac.in/

A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: piRNABank (RRID:SCR_007858) Copy   

•   Source: SciCrunch Registry

http://www.USherbrooke.ca/vers/MtbRegList

A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs.

Proper citation: MtbRegList (RRID:SCR_007811) Copy   

•   Source: SciCrunch Registry

http://caps.ncbs.res.in/MegaMotifbase/index.html

A database of structural motifs for protein structures related at the family and-or superfamily level. Such motifs among structurally aligned proteins are recognized by the conservation of amino acid preference and solvent inaccessibility and are examined for the conservation of other important structural features like secondary structural content, hydrogen bonding pattern and residue packing. These motifs may form the common core by maintaining a particular spatial orientation pattern when compared across different proteins belonging to the same family or superfamily. Such motifs can also be employed to design and rationalize protein engineering and folding experiments. Therefore, the MegaMotifbase can be a useful resource to gain knowledge about structure and functional relationship of proteins. Alignments are available for download.

Proper citation: MegaMotifbase (RRID:SCR_007775) Copy   

•   Source: SciCrunch Registry

http://genesilico.pl/modomics/

A database of RNA modification pathways. The MODOMICS database contains the following types of items: * Modified Bases : Each modified base consists of a unique chemical structure. They are sorted by the regular RNA bases they originate from. The modified base queuosine is special, since it is synthesized first, and then attached to the ribose by a transglycosylation reaction. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). In the download section, the .mol structure files for alare available. * Modification Pathways : Here, we present four pathway graphs showing what modifications emerge from the different bases. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). All lines connecting two modifications are clickable, and show details on a particular reaction. * Enzymes : Lists enzymes that catalyse known reactions between modified bases. In the table, several alternatively used names for the enzymes are given, as well as a list of participating proteins. * Sequences : Shows sequences of RNAs with modifications highlighted. Currently, tRNAs and small and large subunit rRNAs are included in MODOMICS. * Publications : exactly that.

Proper citation: Modomics (RRID:SCR_007804) Copy   

•   Source: SciCrunch Registry

http://m3d.mssm.edu

M3D is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains Affymetrix expression compendia for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis. M3D (Many Microbe Microarrays) was developed by the Gardner Lab at Boston University to facilitate the exchange and analysis of high quality, curated, microbial gene expression data. Currently, the database only includes data obtained using Affymetrix GeneChip technology, because the high quality of the platform facilitates cross-laboratory integration of data sets. The database allows downloading of raw data (CEL files) or preprocessed data that has been uniformly normalized with RMA. M3D also enables convenient web-based expression data exploration and visualization - accessable via the Analysis page.

Proper citation: Many Microbe Microarrays Database (RRID:SCR_007767) Copy   

•   Source: SciCrunch Registry

http://www.earthworms.org

LumbriBASE is aa research tool for both Earthworm biology and environmental pollution monitoring.It provides a simple, easy-to-use access point to the publicly available Lumbricus rubellus sequence and functional data. It is a research tool for both Earthworm biology and environmental pollution monitoring. It is currently being developed by the Worm Consortium.

Proper citation: LumbriBASE (RRID:SCR_007766) Copy   

•   Source: SciCrunch Registry

http://molmovdb.mbb.yale.edu/molmovdb/

MolMovDB is a database that 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. The morph server enables the automatic generation of 2D and 3D animations of a plausible or semi-plausible pathway between two static conformations of a protein subunit, such as those conventionally solved by x-ray crystallography. We believe these animations and associated interpolated pathways will become a valuable research and educational tool, allowing the researcher or educator to quickly visualize the chemical transformation of a protein subunit from one conformation into another. With the server, it is easy to determine quickly whether a valid chemical pathway exists between two protein conformations, as in a protein such as calmodulin, or whether, as is the case with diphtheria toxin, the two conformations have no clearly valid chemical pathway and therefore exist most likely as the result of other processes, such as domain swapping.

Proper citation: MolMovDB - Database of Macromolecular Movements (RRID:SCR_007801) Copy   

•   Source: SciCrunch Registry

http://helix-web.stanford.edu/LPFC/

LPFC is a database of structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LPFC: A Library of Protein Family Cores (RRID:SCR_007765) Copy   

•   Source: SciCrunch Registry

http://www.comparative-legumes.org/

LIS is a publicly accessible legume resource that integrates genetic and molecular data from multiple legume species and enables cross-species genomic, transcript and map comparisons. The intent of the LIS is to help researchers leverage data-rich model plants to fill knowledge gaps across crop plant species and provide the ability to traverse between interrelated data types. LIS, a component of the Model Plant Initiative (MPI), is being developed as part of a cooperative research agreement between the National Center for Genome Resources (NCGR) and the USDA Agricultural Research Service (ARS).

Proper citation: Legume Information System (RRID:SCR_007761) Copy   

•   Source: SciCrunch Registry

http://www.uta.fi/imt/bioinfo/KinMutBase/

KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. The current release of the database contains 582 mutations in 20 tyrosine kinase domains and 13 serine/threonine kinase domains. The database refers 1790 cases from 1322 families. KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns.

Proper citation: KinMutBase: A registry of disease-causing mutations in protein kinase domains (RRID:SCR_007759) Copy   

•   Source: SciCrunch Registry