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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IHM-dictionary Resource Report Resource Website 1+ mentions |
IHM-dictionary (RRID:SCR_016186) | software resource | Software resource for a data representation for integrative/hybrid methods of modeling macromolecular structures. | macromolecule, mmcif, pdb, protein, database, databank, spectroscopy, microscopy, crystallography, proteomic | is related to: PDB-Dev | NSF DBI-1519158 | Free, Available for download | SCR_016186 | 2026-09-03 04:53:30 | 4 | |||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | data repository, service resource, storage service resource | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-09-03 04:53:50 | 36 | |||||||||
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ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data analysis software, data processing software, software application, software resource, software toolkit, standalone software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-09-03 04:53:54 | 10 | ||||||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, software resource, web application | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Brain Institute ; Brazilian Council for Research and Technological Development ; Federal University of Rio Grande do Norte ; Multidisciplinary Environment ; NPAD/UFRN |
Free, Freely available | SCR_016506 | 2026-09-03 04:53:50 | 1 | ||||||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-09-03 04:53:44 | 6 | ||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | data analysis software, data analytics software, data processing software, sequence analysis software, software application, software resource | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 106370Z14; Wellcome Trust 355804783; Wellcome Trust WT083481; Wellcome Trust WT092340 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-09-03 04:53:40 | 133 | ||||||||
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NAT/NCS2 Hound Resource Report Resource Website 1+ mentions |
NAT/NCS2 Hound (RRID:SCR_016473) | NAT, NCS2 | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web server for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. Used to scan, identify and evolutionary classify NAT/NCS2 nucleobase transporter proteins. | protein, sequence, scan, identify, evolutionary, classify, prokaryotic, nucleobase, transporter, protein, amino acid, conserved |
is listed by: OMICtools has parent organization: University of Thessaly; Thessaly; Greece |
DOI:10.1101/332452 | Free, Available to download, Freely available | SCR_016473 | Nucleobase Ascorbate Transporter, NCS2:Nucleobase Cation Symporter 2 | 2026-09-03 04:53:43 | 1 | |||||||
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Thermo Fisher: Nanodrop 1000 Spectrophotometer Resource Report Resource Website 50+ mentions |
Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) | instrument resource | Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution. | ABRF, spectrophotometer, nanodrop, concentration measurement, optical density, DNA, RNA, protein, nanodrop, instrument, equipment |
is listed by: USEDit works with: Thermo Scientific NanoDrop 1000 Software |
Commercially available | https://drive.google.com/file/d/1C1Dj_A1QxQibucCbFNues9EDZebDnx8K/view?usp=drivesdk | SCR_018035, Model_Number_Nanodrop_1000, SCR_020560 | https://www.marshallscientific.com/Nanodrop-ND-1000-Spectrophotometer-p/nd-1000.htm, https://www.selectscience.net/products/nanodrop-1000-spectrophotometer/?prodID=79482#tab-2, http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf | SCR_016517 | NanoDrop 1000, Nanodrop ND-1000, Thermo Scientific NanoDrop 1000, NanoDrop 1000 Spectrophotometer | 2026-09-03 04:53:52 | 89 | ||||||
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-09-03 04:54:00 | 11 | ||||||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, data processing software, software application, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-09-03 04:54:01 | 39 | |||||||||
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metaPocket Resource Report Resource Website 10+ mentions |
metaPocket (RRID:SCR_016653) | analysis service resource, production service resource, service resource, simulation software, software application, software resource | Software tool to identify pockets on protein surface to predict ligand-binding sites. | protein, surface, prediction, ligand, binding, site, identify, pocket | is listed by: OMICtools | EU 7th Framework Marie Curie Actions of International Research Staff Exchange Scheme (IRSES) ; Ministry of Science and Technology (MOST) China |
PMID:19645590 PMID:21636590 |
Free for academic users, Freely available | http://sysbio.zju.edu.cn/metapocket | SCR_016653 | metaPocket, metaPocket 2.0 | 2026-09-03 04:54:08 | 41 | ||||||
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cytoHubba Resource Report Resource Website 100+ mentions |
cytoHubba (RRID:SCR_017677) | data analysis software, data processing software, network analysis software, software application, software resource | Software tool for identifying hub objects and sub-networks from complex interactome. Predicts and explore nodes and subnetworks in given network by several topological algorithms. Provides interface to analyze topology of protein-protein interaction networks, such as human, yeast, rat, mouse, fly etc. Plugin works with Cytoscape 2.6 or above, which requires Java 1.5 or above. | Identify, network, subnetwork, topological, algorithm, analyze, protein, interaction, hub, object, intercome | is a plug in for: Cytoscape | Ministry of Science and Technology (MOST) ; Taiwan |
PMID:25521941 | Free, Available for download, Freely available | http://hub.iis.sinica.edu.tw/cytoHubba/ | SCR_017677 | cytoHubba 1.6 | 2026-09-03 04:54:37 | 451 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | data analysis software, data processing software, software application, software resource | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; European Research Council ; Royal Society ; Wellcome Trust |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-09-03 04:54:59 | 1 | ||||||||
|
Ohio University Genomics Core Facility Resource Report Resource Website |
Ohio University Genomics Core Facility (RRID:SCR_018268) | OUGF | access service resource, core facility, service resource, training service resource | Core provides equipment and services.Equipment available includes AB 3130xl Genetic Analyzer 16 capillary array,Nanodrop 1000 Agilent 2100 Bioanalyzer, Agilent 3100 Off Gel Fractionator, Sage Science Pippin Prep, Aria Mx Real Time PCR machine, Illumina MiSeq, Ion Torrent PGM. Research services include DNA sequencing, fragment and microsatellite analysis, AFLP, SNP screening RNA/DNA quantification, quality control, size distribution, RIN analysis, Protein fraction sizing and quanitification, QA/QC purified protein/antibodies, Low cell consumption two-color flow cytometry analysis, Isoelectric focusing prior to Mass Spec, DIGE analysis, or SDS-PAGE, Automated nucleic acid separation and size collection (90 bp to 1.5 kbp), Relative and Absolute qPCR quantification (SYBR, TaqMan probe), End-point PCR genotyping, fragment melt analysis, copy number determination. Provides Next-Generation Sequencing including total RNA, small RNA, exosome and rRNA-depleted RNAseq, SHAPE-seq, 5-end mapping, de novo genome sequencing and targeted DNA sequencing, ChIP-seq, Methyl-seq, Bioinformatic analysis of NGS data, Custom experimental design, optimization, and consulting. Educational services include Hands on training for any basic lab technique or service used at OUGF, Classroom and research lab lectures and informational seminars, Class and small group tours of facility. | Genetics, equipment, service, core facility, RT PCR, protein, antibody, RNA, DNA, quantification, quality control, genotyping, qPCR, next generation sequencing, USEDit, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Ohio University; Ohio; USA |
ABRF_498 | https://coremarketplace.org/?FacilityID=498 | SCR_018268 | Ohio University Genomics Facility | 2026-09-03 04:55:06 | 0 | |||||||
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BepiPred-2.0 Resource Report Resource Website 1+ mentions |
BepiPred-2.0 (RRID:SCR_018499) | analysis service resource, data access protocol, production service resource, service resource, software application, software resource, standalone software, web service | Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Sequential predictor, B cell epitope, B cell epitope predictor, B-cell epitope, protein sequence, protein, epitope, sequence | has parent organization: Technical University of Denmark; Lyngby; Denmark | NIH HHSN272201200010C | PMID:28472356 PMID:16635264 |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.cbs.dtu.dk/services/BepiPred-1.0/ | SCR_018499 | BepiPred-1.0, BepiPred | 2026-09-03 04:54:59 | 7 | ||||||
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DiscoTope Resource Report Resource Website 100+ mentions |
DiscoTope (RRID:SCR_018530) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server to predict discontinuous B cell epitopes from protein three dimensional structures. | B cell epitope, B cell epitope prediction, discontinous B cell epitope prediction, protein, protein three dimentional structure, protein structure, 3D | European Union Seventh Framework Programme | PMID:23300419 | Free, Freely available | SCR_018530 | 2026-09-03 04:55:00 | 109 | |||||||||
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AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin. | Allergen, allergen prediction, physicochemical protein property, protein, protein property, allergen exposure | National Research Fund of the Ministry of Education and Science ; Bulgaria |
PMID:23735058 | SCR_018496 | 2026-09-03 04:55:08 | 352 | ||||||||||
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ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-09-03 04:55:10 | 109 | |||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-09-03 04:55:11 | 4 | ||||||||
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BpForms Resource Report Resource Website |
BpForms (RRID:SCR_018653) | data access protocol, software resource, software toolkit, web service | Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts. | Molecular structure description, DNA, RNA, protein, modification, epigenetics, transcriptomics, post transcriptional modification, post translational modification, bio.tools |
uses: BcForms is used by: ObjTables is used by: Datanator is listed by: Debian is listed by: bio.tools is related to: BcForms is related to: ObjTables |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bpforms | https://bio.tools/bpforms | SCR_018653 | 2026-09-03 04:55:08 | 0 |
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