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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Thermo Fisher: Qubit fluorimeter Resource Report Resource Website 50+ mentions |
Thermo Fisher: Qubit fluorimeter (RRID:SCR_018095) | instrument resource | Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds. | Invitrogen, benchtop, fluorometer, DNA, RNA, protein, measurement, concentration, assay, instrument, equipment | Restricted | https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0017209_Qubit_4_Fluorometer_UG.pdf | SCR_018095 | Qubit 4 Fluorometer | 2026-09-12 12:58:57 | 53 | |||||||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-09-12 12:58:57 | 90 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | analysis service resource, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-09-12 12:58:57 | 7206 | |||||
|
SARS-CoV-2-Sequences Resource Report Resource Website 10+ mentions |
SARS-CoV-2-Sequences (RRID:SCR_018319) | data or information resource, data repository, data set, service resource, storage service resource | Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released. | SARS-CoV-2, SARS coronavirus, SARS-CoV infection, Coronavirus, data, SARS-CoV-2 sequence collection, nucleotide, genome, Betacoronavirus, protein |
works with: GenBank works with: NCBI Sequence Read Archive (SRA) |
COVID-19 | The Federal Government | Free, Available for download, Freely available | SCR_018319 | Severe Acute Respiratory Syndrome CoronaVirus 2 Sequences | 2026-09-12 12:58:59 | 37 | |||||||
|
HPEPDOCK Server Resource Report Resource Website 50+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
Huazhong University of Science and Technology ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-09-12 12:59:02 | 73 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-09-12 12:59:02 | 316 | |||||||
|
ToxinPred Resource Report Resource Website 100+ mentions |
ToxinPred (RRID:SCR_018542) | analysis service resource, production service resource, service resource, software resource, software toolkit | Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins. | Toxin, toxicity, toxicity prediction, peptide toxicity prediction, peptide design, protein, peptide mutation, toxic region, protein toxic region | Council of Scientific and Industrial Research Govt. of India ; Department of Biotechnology Govt. of India |
PMID:29300301 | Free, Freely available | SCR_018542 | 2026-09-12 12:59:02 | 244 | |||||||||
|
ProteinPilot Software Resource Report Resource Website 1000+ mentions |
ProteinPilot Software (RRID:SCR_018681) | data analysis software, data processing software, software application, software resource | Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems. | Protein identification, protein expression, protein expression analysis, protein, post translational modification, proteomics, mass spectrometry system | Restricted | SCR_018681 | Protein Pilot, Protein Pilot Software | 2026-09-12 12:59:04 | 1489 | ||||||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-09-12 12:59:04 | 0 | ||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 500+ mentions |
Batch Web CD-Search Tool (RRID:SCR_018756) | data access protocol, service resource, software resource, web service | Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence. | Functional domain detection, protein sequence, protein sequence domain, functional domain, protein, nucleotide sequence, conserved domain search, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIH Intramural Research Program | PMID:15215404 | Free, Freely available | biotools:cd-search | https://bio.tools/cd-search | SCR_018756 | NCBI Batch CD Search Tool, Batch conserved domain search, Conserved Domain Search service, CD-search | 2026-09-12 12:59:05 | 838 | |||||
|
PPA-Pred2 Resource Report Resource Website 1+ mentions |
PPA-Pred2 (RRID:SCR_018957) | data access protocol, simulation software, software application, software resource, web service | Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes. | Protein, protein affinity, affinity prediction, predicting binding affinity, protein protein complex, binding affinity | Department of Science and Technology ; Government of India |
PMID:5172924 | Free, Freely available | SCR_018957 | Protein-Protein Affinity Predictor 2 | 2026-09-12 12:59:08 | 8 | ||||||||
|
Vesiclepedia Resource Report Resource Website 100+ mentions |
Vesiclepedia (RRID:SCR_019011) | data or information resource, data repository, database, service resource, storage service resource | Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature. | Extracellular vesicles, gene information, molecule information, protein, RNA, lipid, metabolite, gene ontology, annotation, external references, FASEB list | uses: Entrez Gene | Australian Research Council ; NHMRC project grant |
DOI:10.1371/journal.pbio.1001450 DOI:10.1093/nar/gky1029 |
Free, Freely available | SCR_019011 | Vesiclepedia 2019 | 2026-09-12 12:59:08 | 214 | |||||||
|
FGENESH Plus Resource Report Resource Website 1+ mentions |
FGENESH Plus (RRID:SCR_018937) | data access protocol, simulation software, software application, software resource, web service | Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence. | HMM, gene prediction, protein, multiple gene prediction, genomic DNA, similar protein, protein sequence, Softberry | is related to: Fgenesh plus plus | Free, Freely available | SCR_018937 | Fgenesh plus | 2026-09-12 12:59:08 | 6 | |||||||||
|
MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine. | Qantitative proteomics, mass spectrometry, spectra processes, LC runs, protein, peptide |
uses: Mascot is listed by: SoftCite |
Free, Available for download | http://msquant.alwaysdata.net/ | SCR_019206 | 2026-09-12 12:59:10 | 4 | |||||||||
|
ToRNADo Resource Report Resource Website 100+ mentions |
ToRNADo (RRID:SCR_002706) | data processing software, data visualization software, software application, software resource | A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion. | duplex, protein, rna, visualization | has parent organization: Stanford University; Stanford; California | NIH ; NIGMS R01GM107340; NIGMS U54GM072970 |
Free, Available for download, Freely available | nif-0000-23335 | SCR_002706 | 2026-09-12 01:00:08 | 105 | ||||||||
|
MetaMorph Microscopy Automation and Image Analysis Software Resource Report Resource Website 5000+ mentions |
MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) | MetaMorph | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression. | automated, microscope, acquisition, device, control, image, analysis, fluorescent, cell, signaling, counting, protein, expression, Molecular Devices | PMID:18367250 | Commercially available | SciRes_000136 | SCR_002368 | MetaMorph version 7.8.0.0, Molecular Devices Metamorph Premier Software, MetaMorph image analysis software, MetaMorph Microscopy Automation and Image Analysis Software | 2026-09-12 01:00:08 | 8382 | |||||||
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COnsensus-DEgenerate Hybride Oligonucleotide Primers Resource Report Resource Website 1+ mentions |
COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fractionation, gel, 3', amplification, clone, dna, genome, homolog, human, hybrid, molecule, oligonucleotide, pcr, plant, primer, protein, sequence, transcriptase-methyltransferase |
is related to: OMICtools has parent organization: University of Washington; Seattle; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25557 | SCR_002875 | CODEHOP | 2026-09-12 01:00:09 | 8 | ||||||||
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Autogrid Resource Report Resource Website 1000+ mentions |
Autogrid (RRID:SCR_015982) | data analysis software, data processing software, simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock. | software, automated, docking, analysis, tool, precalculate, set, grid, ligand, protein, target, molecular, simulation, modeling, protein-ligand interaction, data |
is listed by: SoftCite is related to: AutoDock has parent organization: The Scripps Research Institute Labs and Facilities |
The Scripps Research Institute ; San Diego ; California |
PMID:16862531 | THIS RESOURCE IS NO LONGER IN SERVICE | http://mgl.scripps.edu/forum | SCR_015982 | Autogrid toolkit, Autogrid: automated grid | 2026-09-12 12:58:33 | 1261 | ||||||
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ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource, web application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; INBIOMED initiative ; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; University of Vigo 09VIB10 to F.F-.R.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-09-12 12:58:33 | 125 | |||||
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DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-09-12 12:58:34 | 489 |
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