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http://www.noncode.org/

Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences.

Proper citation: NONCODE (RRID:SCR_007822) Copy   

•   Source: SciCrunch Registry

http://networkin.info/

A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions.

Proper citation: NetworKIN (RRID:SCR_007818) Copy   

•   Source: SciCrunch Registry

http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html

The Human BAC Ends Database is a database of sequences from the ends of bacterial artificial chromosome (BAC) clones. A whole genome sequencing approach has been described in a map-as-you-go strategy. The complete sequence of a seed BAC is searched against a BAC end database and the minimally overlapping clones in each direction are selected for sequencing. As coverage increases, BAC end sequences provide samples for whole genome survey. It currently contains 743,000 end sequences from 470,000 clones (20 X clone coverage and 12% sequence coverage), generated by TIGR, UofWashington and CalTech, providing a sequence marker every 5 kb across the genome. The coverage by paired-ends on chromosome 22 is over 5X. The project is funded by DOE.

Proper citation: Human BAC Ends Database (RRID:SCR_007727) 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.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://supfam.org/SUPERFAMILY/

SUPERFAMILY is a database of structural and functional protein annotations for all completely sequenced organisms. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 1,700 completely sequenced genomes against the hidden Markov models.

Proper citation: SUPERFAMILY (RRID:SCR_007952) Copy   

•   Source: SciCrunch Registry

http://stitch.embl.de

Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.

Proper citation: Search Tool for Interactions of Chemicals (RRID:SCR_007947) 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://polya.umdnj.edu/

A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites.

Proper citation: PolyA DB (RRID:SCR_007867) 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.pictar.org

An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets

Proper citation: PicTar (RRID:SCR_003343) Copy   

•   Source: SciCrunch Registry

https://planttfdb.gao-lab.org/

Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

Proper citation: PLANTTFDB (RRID:SCR_003362) Copy   

•   Source: SciCrunch Registry

http://phosphat.uni-hohenheim.de/

Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required).

Proper citation: PhosPhAt (RRID:SCR_003332) Copy   

•   Source: SciCrunch Registry

http://www.xenbase.org/

Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.

Proper citation: Xenbase (RRID:SCR_003280) Copy   

•   Source: SciCrunch Registry

http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

•   Source: SciCrunch Registry

http://www2.mrc-lmb.cam.ac.uk/

The MRC Laboratory of Molecular Biology (LMB) has long been, and remains, a world-class research laboratory. Our primary goal is to understand biological processes at the molecular level, through the application of methods drawn from physics, chemistry and genetics. This quest extends from structural studies of individual macromolecules, through their interactions and beyond to the functioning of subcellular systems, cells and multicellular systems in whole organisms, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. The LMB is one of the birthplaces of modern molecular biology. Many techniques were pioneered at the laboratory, most notably methods for determining the three-dimensional structure of proteins and DNA sequencing. Whole genome sequencing was initiated at the LMB. Another landmark discovery was the invention of monoclonal antibodies. Over the years, the work of LMB scientists has attracted 9 Nobel Prizes, shared between 13 LMB scientists, as well as numerous other prizes and scientific awards.

Proper citation: MRC Laboratory of Molecular Biology (RRID:SCR_003527) Copy   

•   Source: SciCrunch Registry

https://github.com/dbitton/LaSSO

An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.

Proper citation: LaSSO (RRID:SCR_003418) Copy   

•   Source: SciCrunch Registry

http://www.etoxproject.eu/

Project to develop a drug safety database from the pharmaceutical industry legacy toxicology reports and public toxicology data; innovative in silico strategies and novel software tools to better predict the toxicological profiles of small molecules in early stages of the drug development pipeline. The project is creating this pharmaco-toxicological database with an aim to: * Reduce the number of animal tests * Decrease the attrition rates of new drug candidates * Increase the success rate of new molecular entities becoming drugs * Improve the safety of drugs on the market The project consists of three different systems, * eTOX VITIC Database a unified database containing all confidential and non-confidential data collected in eTOX (historical data from the pharmaceutical industry) * ChOX Database a unified database containing public data (literature and public database) * eTOXsys Query and Prediction System an interface providing a uniform access to the two databases (VITIC and ChOX) and to all developed prediction models and systems

Proper citation: eTOX (RRID:SCR_003712) Copy   

•   Source: SciCrunch Registry

http://paleobiodb.org/

A non-governmental, non-profit public database for paleontological data providing researchers and the public with information about the entire fossil record. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database's broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions. Paleontological data files are accepted for upload. However, PaleoBioDB needs some basic data types to be included in order to perform an upload. The Application Programming Interface (API) gives scientists, students, and developers programmatic access to taxonomic, spatial, and temporal data contained within the database.

Proper citation: Paleobiology Database (RRID:SCR_003798) Copy   

•   Source: SciCrunch Registry

http://www.innomed-addneuromed.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.

Proper citation: AddNeuroMed (RRID:SCR_003819) Copy   

•   Source: SciCrunch Registry