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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | SciCrunch Registry | ProtParam | 2026-10-10 12:40:09 | 7206 | |||||
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pepwheel Resource Report Resource Website 1+ mentions |
pepwheel (RRID:SCR_018398) | data access protocol, service resource, software resource, web service | Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation. | Computational proteomics, data analysis pipeline, label free quantification, mass spectrometry, quantitative proteomics, visualise protein sequence, helical wheel diagram, peptice sequence display, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: EMBOSS works with: Proteome Discoverer |
Free, Freely available | biotools:pepwheel | https://bio.tools/pepwheel | SCR_018398 | SciCrunch Registry | 2026-10-10 12:40:54 | 2 | ||||||||
|
TDimpute Resource Report Resource Website 1+ mentions |
TDimpute (RRID:SCR_018306) | data analysis software, data processing software, software application, software resource | Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. | Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/803692 | Free, Available for download, Freely available | biotools:tDimpute, BioTools:TDimpute | https://bio.tools/TDimpute, https://bio.tools/TDimpute, https://bio.tools/TDimpute | SCR_018306 | SciCrunch Registry | 2026-10-10 12:40:12 | 1 | |||||||
|
Protein Interactions Calculator Resource Report Resource Website 10+ mentions |
Protein Interactions Calculator (RRID:SCR_018574) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex. | Protein interaction, interaction calculation, single site, accessible surface are, residue depth, protein surface, residue distance, residue interaction, protein complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Department of Biotechnology Government of India | PMID:17584791 | Free, Freely available | biotools:pic | https://bio.tools/pic | http://crick.mbu.iisc.ernet.in/~PIC | SCR_018574 | SciCrunch Registry | 2026-10-10 12:40:55 | 34 | |||||
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG003749; NIDA U54 DA021519; NIEHS P30 ES06096; NIEHS U01 ES015675; NLM R01 LM008106 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | SciCrunch Registry | 2026-10-10 12:40:16 | 4 | ||||||
|
Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | data access protocol, data or information resource, service resource, software resource, web service | Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. | Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Phytozome is related to: NCBI is related to: Machado |
Embrapa | DOI:10.1101/2020.05.22.110510 | Free, Freely available | biotools:plantannot | https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot | SCR_018429 | SciCrunch Registry | Plantannot v2 | 2026-10-10 12:40:14 | 1 | ||||
|
GalaxyWEB Resource Report Resource Website 100+ mentions |
GalaxyWEB (RRID:SCR_018558) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined. | Protein structure prediction, protein structure refinement, protein sequence, template based modeling, model structure, loop location, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
Ministry of Land ; Transport and Maritime Affairs of Korea ; National Research Foundation of Korea ; Seoul National University |
PMID:22649060 | Free, Freely available | biotools:galaxyweb | https://bio.tools/galaxyweb | SCR_018558 | SciCrunch Registry | 2026-10-10 12:40:55 | 231 | ||||||
|
MaxAlign Resource Report Resource Website 10+ mentions |
MaxAlign (RRID:SCR_018552) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area. | Maximizing data, post process alignment, gap free column alignment area, sequence subset selection, improve alignment area, bio.tools |
is listed by: Debian is listed by: bio.tools |
Foundation for Science and Technology Portuguese Ministry of Science. | PMID:17725821 | Free, Available for download, Freely available | biotools:maxalign | https://bio.tools/maxalign | SCR_018552 | SciCrunch Registry | MaxAlign 1.1, MaxAlign 1.1 Server | 2026-10-10 12:40:21 | 11 | |||||
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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 | SciCrunch Registry | 2026-10-10 12:40:16 | 73 | ||||||
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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 | SciCrunch Registry | 2026-10-10 12:40:21 | 316 | |||||||
|
EpiEstim Resource Report Resource Website 10+ mentions |
EpiEstim (RRID:SCR_018538) | data analysis software, data processing software, software application, software resource, software toolkit | Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series. | Estimate time varying, reproduction number, epidemics, quantify transmissibility, time series analysis, reproductionc number analysis, incidence time series, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
United Kingdom Medical Research Council | PMID:24043437 | Free, Available for download, Freely available | biotools:EpiEstim | https://bio.tools/EpiEstim | SCR_018538 | SciCrunch Registry | Estimate Time Varying Reproduction Numbers from Epidemic Curves | 2026-10-10 12:40:55 | 35 | |||||
|
betaVAEImputation Resource Report Resource Website 1+ mentions |
betaVAEImputation (RRID:SCR_018730) | data analysis software, data processing software, software application, software resource | Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis. | Genomic data, handling missing data, deep learning framework, variational autoencoder, imputing missing values, transcriptome, methylome, data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:betavaeimputation | https://bio.tools/betavaeimputation | SCR_018730 | SciCrunch Registry | 2026-10-10 12:40:19 | 2 | ||||||||
|
CRISPR-ERA Resource Report Resource Website 10+ mentions |
CRISPR-ERA (RRID:SCR_018710) | data access protocol, service resource, software resource, web service | Software comprehensive design tool for CRISPR mediated gene editing, repression and activation. Fast and comprehensive guide RNA design tool for genome editing, repression and activation. Used for automated genome wide sgRNA design. | Design tool, CRISPR mediated gene editing, gene repression, gene activation, guide RNA design, genome, automated genome, sgRNA design, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
FANEDD ; NIDA R01 DA036858; NIDCR ; NIH Office of The Director ; NIH Office of the Director OD017887; NSFC |
PMID:26209430 | Free, Freely available | biotools:CRISPR-ERA | https://bio.tools/CRISPR-ERA | SCR_018710 | SciCrunch Registry | CRISP-Editing, Repression and Activation | 2026-10-10 12:40:25 | 13 | |||||
|
MiXCR Resource Report Resource Website 50+ mentions |
MiXCR (RRID:SCR_018725) | data analysis software, data processing software, software application, software resource | Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling. | Process immunome data, raw sequence, quantitated clonotype, B cell receptor, sequencing data analysis, T cell receptor, high throughput sequencing data, adaptive immunity profiling, MiLaboratory, bio.tools |
is listed by: Debian is listed by: bio.tools |
Russian Science Foundation | PMID:25924071 | Restricted | biotools:MiXCR, BioTools:MiXCR | https://github.com/milaboratory/mixcr, https://bio.tools/MiXCR, https://bio.tools/MiXCR, https://bio.tools/MiXCR | SCR_018725 | SciCrunch Registry | 2026-10-10 12:40:57 | 73 | ||||||
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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 | SciCrunch Registry | 2026-10-10 12:40:18 | 0 | ||||||
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precrec Resource Report Resource Website 1+ mentions |
precrec (RRID:SCR_018659) | data analytics software, software application, software resource, software toolkit | Software R package for fast and accurate precision recall and ROC curve calculations. Calculates accurate precision recall and Receiver Operator Characteristics curves. | Precision recall, receiver operator characteristics, receiver operator characteristics curve, curve calculations, precision recall calculation, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN |
DOI:10.1093/bioinformatics/btw570 | Free, Freely available | biotools:precrec | https://bio.tools/precrec | SCR_018659 | SciCrunch Registry | 2026-10-10 12:40:18 | 2 | |||||||
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Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | application programming interface, data access protocol, data or information resource, database, software resource, web application | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | SciCrunch Registry | 2026-10-10 12:40:18 | 2 | ||||||
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PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | analysis service resource, data or information resource, database, production service resource, service resource | Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets. | Kyushu Institute of Technology, meta analysis, prognostic gene value, cancer microarray dataset, clinical annotation, gene expression, tumor marker, therapeutic target, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:19393097 | Free, Freely available | SCR_018741, biotools:prognoscan | http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html, https://bio.tools/prognoscan | SCR_018740 | SciCrunch Registry | 2026-10-10 12:40:57 | 461 | |||||||
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Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | SciCrunch Registry | EVcouplings | 2026-10-10 12:40:19 | 26 | |||||
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StoatyDive Resource Report Resource Website 1+ mentions |
StoatyDive (RRID:SCR_018796) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data. | Evaluate predicted peak profile, classify predicted peak profile, assess binding specificity, protein-target specificity, sequencing data, CLIP-seq data, CHIP-Seq data, peak profile data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | SCR_018800, biotools:StoatyDive | https://bio.tools/StoatyDive | SCR_018796 | SciCrunch Registry | 2026-10-10 12:40:27 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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