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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PROVEAN Resource Report Resource Website 1000+ mentions |
PROVEAN (RRID:SCR_002182) | PROVEAN | data analysis service, software resource, service resource, production service resource, analysis service resource | A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. | amino acid substitution, indel, function, protein, amino acid, substitution, protein variant, genome variant, next-generation sequencing, insertion, deletion |
is listed by: OMICtools has parent organization: J. Craig Venter Institute |
NIH ; NHGRI 5R01HG004701-04 |
PMID:23056405 | Free, Available for download, Freely available | OMICS_01849 | SCR_002182 | Protein Variation Effect Analyzer | 2026-02-15 09:18:15 | 2231 | |||||
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University of Utah Genetic Science Learning Center - Learn Genetics Resource Report Resource Website 1+ mentions |
University of Utah Genetic Science Learning Center - Learn Genetics (RRID:SCR_001910) | Learn.Genetics, Learn Genetics | video resource, training material, training resource, slide, data or information resource, narrative resource | Educational resources that provide accurate and unbiased information about topics in genetics, bioscience and health for global and local audiences. They are jargon-free, target multiple learning styles, and often convey concepts through animation and interactivity. The Genetic Science Learning Center is a science and health education program located in the midst of the bioscience research being carried out at the University of Utah. Our mission is making science easy for everyone to understand. * Two websites, available free of charge to Internet users worldwide: ** Learn.Genetics delivers educational materials on genetics, bioscience and health topics. They are designed to be used by students, teachers and members of the public. The materials meet selected US education standards for science and health. ** Teach.Genetics provides resources for K-12 teachers, higher education faculty, and public educators. These include PDF-based Print-and-Go™ activities, unit plans and other supporting resources. The materials are designed to support and extend the materials on Learn.Genetics. *Professional development programs that update K-16 teachers' expertise in bioscience and health topics as well as prepare them to implement the materials on our websites. * Community programs that engage with diverse communities in discussions about genetics and health, and in developing culturally and linguistically-appropriate educational materials. Some topics in genetics and bioscience research are controversial. The Center does not take sides in political or ethical controversies. Rather, our goal is to provide comprehensive information that promotes a lively discussion of these topics, so that individuals can arrive at their own informed decisions. | gene, dna, protein, education, genetics, science, bioscience, health, teacher, student, public, professional development, k-12, undergraduate, lesson plan, heredity, genetic trait, cell, molecule, stem cell, cloning, gene therapy, transgenic mouse, epigentics, addiction, genetic variation |
has parent organization: University of Utah; Utah; USA is parent organization of: New Science of Addiction: Genetics and the Brain |
NIH Office of the Director R25OD021903 | You are granted a revocable license to download and print hard copy versions of the material contained on the site for your personal, Educational and noncommercial use, Provided you do not modify or delete any copyright or other notice that appears on the material you download or print. | nif-0000-10482 | http://learns.genetics.utah.edu/ | SCR_001910 | University of Utah Genetic Science Learning Center, Genetic Science Learning Center - Learn.Genetics, Genetic Science Learning Center, Genetic Science Learning Center - Learn Genetics | 2026-02-15 09:18:12 | 9 | |||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | database, service resource, storage service resource, data repository, data or information resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-02-15 09:18:12 | 8 | ||||
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Parasite genome databases and genome research resources Resource Report Resource Website 1+ mentions |
Parasite genome databases and genome research resources (RRID:SCR_008150) | topical portal, data or information resource, database, portal | This website contains information about the genomic sequence of parasites. It also contains multiple search engines to search six frame translations of parasite nucleotide databases for motifs, parasite protein databases for motifs, and parasite protein databases for keywords and text terms. * Guide to Internet Access to Parasite Genome Information * Guide to web-based analysis tools * Parasite Genome BLAST Server: Search a range of parasite specific nucleotide sequence databases with your own sequence. * Parasite Proteome Keyword Search Facility: Search parasite protein databases for keywords and text terms * Parasite Proteome Motif Search Facility: Search parasite protein databases for motifs * Parasite Six Frame Translation Motif Search Facility: Search six frame translations of parasite nucleotide databases for motifs * Genome computing resources: A list of ftp and gopher sites where genome computing applications and other resources can be found. | genome, genomic, nucleotide, parasite, protein, proteome, sequence, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-20981 | SCR_008150 | Parasite Genome Database | 2026-02-15 09:19:44 | 2 | |||||||||
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Protein Databank Fun Resource Report Resource Website 1+ mentions |
Protein Databank Fun (RRID:SCR_008226) | software application, data processing software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PDBfun is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. PDBfun is an integrated web tool for querying the PDB at the residue level and for local structural comparison. It integrates knowledge on single residues in protein structures coming from other databases or calculated with available or in-house developed instruments for structural analysis. Each set of different annotations represents a feature. Features are listed in PDBfun main page in orange. Features can be used for building residues selections. | functional, 2d, ability, activity, analysis, binding, catalytic, cavity, chain, cleft, domain, ligand, location, motif, protein, protein structure databases, residue, secondary, sequence, size, solvent, structural, structure, surface | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21315 | SCR_008226 | PDBfun | 2026-02-15 09:19:45 | 2 | |||||||||
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Human Hereditary Diseases of Proteolysis Resource Report Resource Website 1+ mentions |
Human Hereditary Diseases of Proteolysis (RRID:SCR_008344) | disease-related portal, topical portal, data or information resource, portal | This resource has cataloged a total of 80 human hereditary diseases caused by mutations in protease-coding genes, which implies that more than 10% of the human protease genes are involved in human pathologies. They are classified in three groups: loss of function, gain of function, and an heterogeneous group including non-protease homologs (np), putative proteases, and hedgehog proteins with only autoprocessing activity. Type of inheritance is indicated by R (recessive) or D (dominant). | gene, disease, dominant, hereditary, homolog, human, protease, protein, proteolysis, recessive | has parent organization: University of Oviedo; Oviedo; Spain | nif-0000-25562 | SCR_008344 | Diseases of Proteolysis | 2026-02-15 09:19:47 | 2 | |||||||||
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Protein Subcellular Location Image Database Resource Report Resource Website |
Protein Subcellular Location Image Database (RRID:SCR_008663) | PSLID | database, data set, service resource, storage service resource, data repository, image analysis service, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees. The annotations in PSLID provide a description of sample preparation and fluorescence microscope imaging. |
protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, subcellular localization, 3d spatial image, 2d spatial image, micrograph, content-based retrieval, green fluorescent protein |
is listed by: 3DVC is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Merck Company Foundation ; NIGMS GM075205; NCI R33 CA83219; NSF MCB-8920118 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33313 | SCR_008663 | PSLID - Protein Subcellular Location Image Database, Protein Subcellular Location Image Database | 2026-02-15 09:19:53 | 0 | ||||||
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Quertle: Relationship-Driven Biomedical Search Resource Report Resource Website |
Quertle: Relationship-Driven Biomedical Search (RRID:SCR_008676) | portal, database, research forum portal, data or information resource, topical portal, disease-related portal | Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. Quertle''s friendly interface makes it simple to search and refine results. Using advanced semantics, Quertle finds quality results, not just long lists. And it hods: all of PubMed, a growing number of full-text documents, news, and more. Features: :- Find Relationships, not Just :- Focus on Core Concepts: Since Quertle searches for Relationships, all the terms in your query must be found together in a meaningful way. Thus, Quertle immediately gives you results with more relevance. :- Unleash the Strength of Power Terms: Use Power Terms to search for categories of objects. For instance, you can use Protein to search for any protein, rather than the occurrence of the term, protein. View all Power Terms. :- Search Full-text Documents: The Quertle search engine has been optimized to search full-text documents, including the Material and Methods section (but not the Bibliography). :- Use Real Biology & Chemistry Terms: Quertle recognizes capital TWIST as the transcription factor (not the verb), and capital NO as nitrous oxide(not a negative). So, use proper capitalization in your query, and you won''t be lost in a sea of irrelevant results. :- Look for the Quertle Difference on the Results Page : More relevant results : Easy filtering and breadcrumb tracking : Automatic identification of key concepts : Single-click access to PDFs of full-text documents :Keyword: Biomedical, Search engine, Database, Researcher, Linguistic, Technology, Semantic, Relationship, Protein, Biology, Chemistry, : | all the terms in your query must be found together in a meaningful way. thus, biology, chemistry, chemistry terms: quertle recognizes capital twist as the transcription factor (not the verb), database, if you search for two or more terms, including the material and methods section (but not the bibliography). - use real biology &, linguistic, not just the terms scattered within the same document. - focus on core concepts: since quertle searches for relationships, protein, quertle immediately gives you results with more relevance. - unleash the strength of power terms: use power terms to search for categories of objects. for instance, rather than the occurrence of the term, relationship, researcher, search engine, semantic, technology, use proper capitalization in your query, you can use protein to search for any protein, you will find occurrences of a conceptual relationship | nif-0000-33690 | SCR_008676 | Quertle | 2026-02-15 09:19:52 | 0 | ||||||||||
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mtocDB Resource Report Resource Website |
mtocDB (RRID:SCR_008933) | mtocDB | image collection, data or information resource, database | A database of over 300 Electron Microscopy (EM) images of centrioles and centriole related structures from almost 60 species, described by a controlled vocabulary allowing detailed description of the observed structures. This knowledge is supplemented by a manually curated list of proteins known to be involved in centriole assembly, their (putative) orthologs, and localization information. mtocDB aims to characterize the naturally occurring morphological variation observed in centrioles and centriole associated structure alongside molecular information on the proteins involved in their assembly. Examining these in an evolutionary context will allow the cell biology community to infer meaningful relationships between cellular assembly mechanisms and the structures they form. This community resource for cell biologists interested in the the evolution of centrioles and centriole related structures aims to bridge the gap between structural morphology and molecular function by examining naturally occurring structural variation in a phylogenomic context. Centrioles are cylindrical microtubule arrays required for stability and duplication of the centrosome in animal cells, and for the assembly of cilia and flagella in many eukaryotes. The presence of centrioles throughout most eukaryotic branches suggests that this structure was present in the last eukaryotic common ancestor. Although centrioles show a typically well conserved structure, they can perform several functions and display a diversity of accessory structures. However, this diversity is not properly classified beyond model organisms, and the information contained in decades of electronic microscopy of other organisms remains untapped. | centriole, morphological variation, morphology, cell biology, cellular assembly, mechanism, structure, evolution, proteomics, genome, ortholog, electron microscopy, protein, centriole assembly, localization, microtubule, image, electron micrograph, micrograph | has parent organization: Instituto Gulbenkian de Ciencia; Oeiras; Portugal | Developed as a community resource, But as of 6/1/13, Requires an account pending resolution of copyright issues | nlx_151804 | SCR_008933 | Microtubule Organizing Center Database | 2026-02-15 09:20:00 | 0 | |||||||
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Molecular Libraries Program Resource Report Resource Website 10+ mentions |
Molecular Libraries Program (RRID:SCR_008847) | MLP | organization portal, portal, service resource, production service resource, data or information resource, material analysis service, topical portal, analysis service resource | High throughput screening services to identify small molecules that can be optimized as chemical probes to study the functions of genes, cells, and biochemical pathways, along with medicinal chemistry and informatics. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. The NIH Molecular Libraries Initiative NIH is designed to discover small molecules that interact with biologically important proteins and pathways and to provide open access to the bioassay and chemical data generated by its research centers. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. As these HTS Technologies were not previously available to the public sector, many investigators may not be familiar with the components and requirements of high throughput screening. A key challenge is to identify small molecules effective at modulating a given biological process or disease state. The Molecular Libraries Roadmap, through one of its components, the Molecular Libraries Probe Production Centers Network (MLPCN), offers biomedical researchers access to the large-scale screening capacity, along with medicinal chemistry and informatics necessary to identify chemical probes to study the functions of genes, cells, and biochemical pathways. This will lead to new ways to explore the functions of genes and signaling pathways in health and disease. There are two kinds of data that are available to the scientific community through a dedicated database: Chemical Compounds and Bioassay Results (NCBI). Various types of data, including informative records on substances, compound structures, and biologically active properties of small molecules are housed respectively within PubChem''''s three primary databases: PCSubstance, PCCompound, and PCBioAssay. To date, PubChem contains over 11 million substance records, details about approximately 5.5 million unique compound structures with links to bioassay descriptions, relevant literature, references, and assay data points and over 250 bioassays, a good percentage of which were contributed by the pilot phase of the MLP. The deposition will continue during the current MLPCN phase. NIH anticipates that these projects will also facilitate the development of new drugs, by providing early stage chemical compounds that will enable researchers in the public and private sectors to validate new drug targets, which could then move into the drug-development pipeline. This is particularly true for rare diseases, which may not be attractive for development by the private sector. Funding opportunities are available through the site. | molecule, compound, probe, small molecule, high throughput screening, gene, cell, biochemical pathway, drug development, protein, pathway |
is used by: LINCS Information Framework is related to: BARD is related to: NIH Clinical Collection is related to: PubChem has parent organization: National Institutes of Health |
NIH | nlx_146246 | SCR_008847 | Molecular Libraries, Molecular Libraries Initiative | 2026-02-15 09:19:57 | 15 | |||||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | software application, data analysis service, software resource, service resource, production service resource, analysis service resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-02-15 09:19:56 | 601 | |||||
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PSIPRED Resource Report Resource Website 1000+ mentions |
PSIPRED (RRID:SCR_010246) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences. | Predict Secondary Structure, protein analysis, secondary structure prediction, protein sequence, sequence analysis, protein, analysis |
is listed by: Debian is listed by: SoftCite has parent organization: University College London; London; United Kingdom |
Biotechnology and Biological Science Research Council ; University College London |
DOI:10.1093/nar/gkz297 | Free, Freely available | SCR_018546, nlx_156884 | https://sources.debian.org/src/psipred/ | SCR_010246 | PSIPRED Protein Sequence Analysis Workbench, PSIPRED 4.0 | 2026-02-15 09:20:18 | 1688 | |||||
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AgingDB Resource Report Resource Website |
AgingDB (RRID:SCR_010226) | AgingDB | database, service resource, storage service resource, data repository, data or information resource | A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments. | oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factor |
is related to: Gene Ontology has parent organization: Pusan National University; Busan; South Korea |
Aging | PMID:23604914 | The community can contribute to this resource | nlx_156773 | http://aging.pharm.pusan.ac.kr/AgingDB/ | SCR_010226 | Aging Database, Aging DB | 2026-02-15 09:20:16 | 0 | ||||
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PlnTFDB Resource Report Resource Website 100+ mentions |
PlnTFDB (RRID:SCR_010899) | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Public database arising from efforts to identify and catalogue all plant genes involved in transcriptional control.Integrative plant transcription factor database that provides web interface to access large sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa (poplar), Oryza sativa (rice), Chlamydomonas reinhardtii and Ostreococcus tauri. Provides access point to its daughter databases of species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags, domain architecture and scientific literature is provided for each family. | protein model, protein sequence, gene family, protein, transcriptional control, blast, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
University of Potsdam ; Germany ; German Federal Ministry of Education and Research ; Fond der Chemischen Industrie |
PMID:19858103 PMID:17286856 |
Free, Freely available | biotools:plntfdb, OMICS_00561 | http://plntfdb.bio.uni-potsdam.de/v3.0/ https://bio.tools/plntfdb |
SCR_010899 | Plant Transcription Factor Database, PlnTFDB v3.0 | 2026-02-15 09:20:21 | 201 | |||||
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Evex Resource Report Resource Website 10+ mentions |
Evex (RRID:SCR_010509) | software application, database, software resource, text-mining software, data or information resource | EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full texts. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene normalization results, allowing straightforward integration with external resources. Further, gene families from Ensembl and HomoloGene provide homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature. | gene, protein, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium |
biotools:evex, nlx_158731 | https://bio.tools/evex | SCR_010509 | 2026-02-15 09:19:59 | 18 | |||||||||
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Thermo Scientific NanoDrop Lite Spectrophotometer Resource Report Resource Website 1+ mentions |
Thermo Scientific NanoDrop Lite Spectrophotometer (RRID:SCR_025369) | instrument resource | Compact, personal UV-Vis microvolume spectrophotometer that complements the full-featured NanoDrop 2000/2000c and NanoDrop 8000 instruments. | UV-Vis microvolume spectrophotometer, DNA, RNA, protein |
is related to: Thermo Scientific NanoDrop 8000 Spectrophotometer is related to: Thermo Scientific NanoDrop 2000c Spectrophotometer is related to: Thermo Scientific NanoDrop 2000 Spectrophotometer |
Model_Number_NanoDrop_Lite | https://www.marshallscientific.com/v/vspfiles/specs/Thermo%20Scientific%20NanoDrop%20Lite%20Spectrophotometer%20-%20Marshall%20Scientific.pdf | SCR_025369 | NanoDrop Lite Spectrophotometer | 2026-02-14 02:09:02 | 5 | ||||||||
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Philius Resource Report Resource Website |
Philius (RRID:SCR_004625) | Philius | data analysis service, software resource, service resource, production service resource, analysis service resource | Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions. | hidden markov model, protein type, segment, topology, confidence metric, prediction, protein, transmembrane, signal peptide, peptide, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:18989393 | nlx_62426, biotools:philius | https://bio.tools/philius | SCR_004625 | 2026-02-15 09:18:46 | 0 | |||||||
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Proteopedia - Life in 3D Resource Report Resource Website 1+ mentions |
Proteopedia - Life in 3D (RRID:SCR_004647) | Proteopedia | data or information resource, narrative resource, wiki | Free, collaborative 3D, interactive encyclopedia of proteins and other molecules, it collects, organizes and disseminates structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists. With a free user account, users can edit pages in Proteopedia. Click on the green links to change the 3D image or click and drag the molecules. Categories include Diseases & Related Topics, Enzymes, Gene Expression & Replication, Metabolism, Signaling & Transport, Structural Biology and Miscellaneous. Currently, Proteopedia has 93,912 articles (pages), and 2,366 registered users (May 2013). Among other pages, Proteopedia contains one page (or article) for every entry in the World Wide Protein Data Bank. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are seeded automatically to include a default view of the asymmetric unit, the abstract of the publication, green links to sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random page, you nearly always get one of these automatically-seeded, PDB-code-titled pages (click Random Page in the navigation box at the upper left), because of their abundance. In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure. | protein, molecule, 3d, rna, dna, structure, function, nucleic acid, biomolecule, structural annotation, 3d visualization, visualization, disease, enzyme, gene expression, replication, metabolism, signaling, transport, structural biology, 3d spatial image | is related to: Worldwide Protein Data Bank (wwPDB) | Divadol Foundation ; Nalvyco Foundation ; Bruce Rosen Foundation ; Jean and Julia Goldwurm Memorial Foundation ; European Union 6th Framework ISSG-CT-2007-037198; European Union 6th Framework LSHG-CT-2006-031220 |
PMID:21567857 PMID:21536137 PMID:19117028 PMID:18673581 |
Free, The community can contribute to this resource | nlx_64233 | SCR_004647 | 2026-02-15 09:18:46 | 8 | ||||||
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SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | data analysis service, database, software resource, data access protocol, web service, service resource, production service resource, data or information resource, analysis service resource | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/ https://bio.tools/smart |
SCR_005026 | Simple Modular Architecture Research Tool | 2026-02-15 09:18:53 | 6760 | ||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | software application, sequence analysis software, data processing software, software resource, data access protocol, web service, data analysis software | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov https://bio.tools/blast https://sources.debian.org/src/ncbi-blast+/ |
SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-02-15 09:18:56 | 15381 |
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