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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RAMPAGE Resource Report Resource Website 100+ mentions |
RAMPAGE (RRID:SCR_017590) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure. | Ramachandran, plot, analysis, upload, PDB, file, coputing, dihedral, angle, extracting, sequence, protein, amino acid, residue, structure | has parent organization: University of Cambridge; Cambridge; United Kingdom | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_017590 | 2026-08-05 10:46:49 | 124 | ||||||||||
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vbSPT Resource Report Resource Website 1+ mentions |
vbSPT (RRID:SCR_017554) | software resource, data processing software, software application, data analysis software | Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants. | Analysis, single, particle, diffusion, trajectory, Markov, short, molecule, intracellularly, protein, data, transition, state | PMID:23396281 | Free, Available for download, Freely available | https://sourceforge.net/projects/vbspt/files/latest/download?source=files | SCR_017554 | variational Bayes single particle tracking | 2026-08-05 10:46:54 | 3 | ||||||||
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MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | data processing software, image analysis software, software application, alignment software, software resource | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-08-05 10:46:58 | 480 | |||||
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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, storage service resource, 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 | 2026-08-05 10:47:00 | 28 | |||||||
|
MascotScan Resource Report Resource Website 10+ mentions |
MascotScan (RRID:SCR_018201) | software resource, data processing software, software application, data analysis software | Software tool for analysis of qualitative data, operating on basis of lists of peptides and proteins identified in samples generated by Mascot database system. Responsible for preparing data for quantitative analysis of proteins both with use of stable isotope labeling and without isotope labeling. | Data analysis, qualitative data, peptide, protein, Mascot database system, stable isotope labeling, no isotope labeling |
is related to: Mascot has parent organization: Warsaw University of Technology; Warsaw; Poland |
Free, Freely available | SCR_018201 | MScan | 2026-08-05 10:46:59 | 10 | |||||||||
|
PROMALS3D Resource Report Resource Website 10+ mentions |
PROMALS3D (RRID:SCR_018161) | data processing software, data access protocol, image analysis software, software application, alignment software, software resource, web service | Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints. | Structure alignment, 3D structure, sequence, protein, amino acid, homolog identification | DOI:10.1093/nar/gkn072 | Free, Freely available | SCR_018161 | 2026-08-05 10:46:57 | 44 | ||||||||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | 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 | 2026-08-05 10:47:00 | 62 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | data processing software, software application, data analysis software, sequence analysis software, software resource, production service resource, service resource, analysis service 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 | 2026-08-05 10:46:56 | 5406 | |||||
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HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | 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 |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-08-05 10:47:04 | 46 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | web service, data access protocol, software resource, production service resource, service resource, analysis service resource | 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 | 2026-08-05 10:47:02 | 248 | |||||||
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ToxinPred Resource Report Resource Website 100+ mentions |
ToxinPred (RRID:SCR_018542) | software toolkit, software resource, production service resource, service resource, analysis service resource | 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 | Department of Biotechnology Govt. of India ; Council of Scientific and Industrial Research Govt. of India |
PMID:29300301 | Free, Freely available | SCR_018542 | 2026-08-05 10:47:02 | 161 | |||||||||
|
ProteinPilot Software Resource Report Resource Website 1000+ mentions |
ProteinPilot Software (RRID:SCR_018681) | software resource, data processing software, software application, data analysis software | 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 | 2026-08-05 10:47:05 | 1487 | ||||||||||
|
BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | software toolkit, data access protocol, software resource, 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 | 2026-08-05 10:47:03 | 0 | ||||||
|
Batch Web CD-Search Tool Resource Report Resource Website 100+ 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 | 2026-08-05 10:47:05 | 368 | |||||
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PPA-Pred2 Resource Report Resource Website 1+ mentions |
PPA-Pred2 (RRID:SCR_018957) | data access protocol, software application, simulation software, 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 | 2026-08-05 10:47:07 | 5 | ||||||||
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Vesiclepedia Resource Report Resource Website 100+ mentions |
Vesiclepedia (RRID:SCR_019011) | data or information resource, data repository, database, storage service resource, 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 | 2026-08-05 10:47:08 | 149 | |||||||
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FGENESH Plus Resource Report Resource Website 1+ mentions |
FGENESH Plus (RRID:SCR_018937) | data access protocol, software application, simulation software, 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 | 2026-08-05 10:47:08 | 6 | |||||||||
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MSQuant Resource Report Resource Website 1+ mentions |
MSQuant (RRID:SCR_019206) | data processing software, software application, data analysis software, software resource, data analytics software | 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 | 2026-08-05 10:47:11 | 4 | |||||||||
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PomBase Resource Report Resource Website 100+ mentions |
PomBase (RRID:SCR_006586) | PomBase | data or information resource, service resource, database | Model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation. PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation, mailing lists, and welcomes data submissions. | fission yeast, gene ontology, genome sequence, schizosaccharomyces pombe (4896), schizosaccharomyces pombe, dna, protein, cosmic assembly, intron, go, chromosome, telomere, centromere, mating region, data mapping, model organism, genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: AmiGO is related to: GeneDB Spombe has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: University College London; London; United Kingdom is parent organization of: Fission Yeast Phenotype Ontology is parent organization of: Pompep |
Wellcome Trust WT090548MA | PMID:22039153 | Public, Acknowledgement requested | biotools:pombase, nlx_144356, r3d100011478 | https://bio.tools/pombase, https://doi.org/10.17616/R3NS78 | http://www.sanger.ac.uk/Projects/S_pombe/ | SCR_006586 | Schizosaccharomyces pombeGenome Sequencing Project | 2026-08-05 10:44:29 | 362 | |||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | data or information resource, web service, data access protocol, database, software resource, data analysis service, production service resource, service resource, analysis service resource | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-08-05 10:44:30 | 7000 |
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