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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | data access protocol, production service resource, analysis 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 | 2026-02-17 10:03:49 | 104 | |||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-17 10:03:10 | 3 | |||||||
|
PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | data analysis software, software application, data processing software, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-02-17 10:03:51 | 75 | |||||||||
|
ConPlot Resource Report Resource Website 1+ mentions |
ConPlot (RRID:SCR_019216) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein. | Residue contact predictions, protein, secondary structure predictions, transmembrane helical topology, sequence conservation, protein bioinformatics, analysing data |
is related to: CCP4 has parent organization: University of Liverpool; Liverpool; United Kingdom |
Restricted | SCR_019216 | 2026-02-17 10:03:53 | 2 | ||||||||||
|
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility Resource Report Resource Website |
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) | BCF | data or information resource, production service resource, analysis service resource, database, service resource, core facility, access service resource, data analysis service | Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services. | metagenomics, proteomics, protein, structure, functional, genomics, programming, scripting, data | Restricted | SCR_017152 | BCF, Core Facility, University of Oslo, Rikshospitalet-Radiumhospitalet, Bioinformatics | 2026-02-17 10:03:32 | 0 | |||||||||
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MoRDa Resource Report Resource Website 1+ mentions |
MoRDa (RRID:SCR_017278) | software application, data or information resource, data processing software, data analysis software, database, software resource, software toolkit | Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline. | molecular, replacement, protein, structure, data, Xray, crystallography | uses: CCP4 | DOI:10.1107/S2053273315099672 | Restricted | https://ccp4serv7.rc-harwell.ac.uk/ccp4online/ | SCR_017278 | Automatic Molecular Replacement Pipeline | 2026-02-17 10:03:33 | 6 | |||||||
|
PatchDock Resource Report Resource Website 50+ mentions |
PatchDock (RRID:SCR_017589) | data access protocol, software application, software resource, web service, simulation software | Web server for molecular docking. Performs structure prediction of protein–protein and protein–small molecule complexes. Molecular docking algorithm based on shape complementarity principles. | Molecular, docking, structure, prediction, protein, molecule, shape, complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Israel Science Foundation ; Hermann Minkowski-Minerva Center for Geometry at Tel Aviv University ; Israeli Ministry of Science ; National Cancer Institute ; NIH |
PMID:15980490 | Free, Freely available | biotools:patchdock | https://bio.tools/patchdock | SCR_017589 | 2026-02-17 10:03:36 | 85 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | data analysis software, software application, data processing software, 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 ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-02-17 10:03:02 | 1 | ||||||||
|
cytoHubba Resource Report Resource Website 100+ mentions |
cytoHubba (RRID:SCR_017677) | software application, data processing software, data analysis software, software resource, network analysis software | 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 | 2026-02-17 10:03:17 | 356 | ||||||
|
BepiPred-2.0 Resource Report Resource Website 1+ mentions |
BepiPred-2.0 (RRID:SCR_018499) | data access protocol, software application, standalone software, production service resource, analysis service resource, service resource, software resource, 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 | 2026-02-17 10:03:05 | 4 | ||||||
|
DiscoTope Resource Report Resource Website 50+ mentions |
DiscoTope (RRID:SCR_018530) | data access protocol, production service resource, analysis 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 | 2026-02-17 10:03:49 | 99 | |||||||||
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AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | data access protocol, production service resource, analysis 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 | 2026-02-17 10:03:29 | 225 | ||||||||||
|
WoLF PSORT Resource Report Resource Website 100+ mentions |
WoLF PSORT (RRID:SCR_002472) | WoLF PSORT | data analysis service, production service resource, analysis service resource, service resource | Data analysis service for protein subcellular localization prediction. | subcellular localization, protein | is listed by: OMICtools | Restricted | OMICS_01637 | SCR_002472 | WoLF PSORT - Protein Subcellular Localization prediction | 2026-02-17 09:59:57 | 129 | |||||||
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AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | data analysis service, production service resource, analysis service resource, service resource | Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. | dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Eotvos Lorand University; Budapest; Hungary |
PMID:24144838 | Acknowledgement requested, Free, Public | biotools:amphoranet, OMICS_01450 | https://bio.tools/amphoranet | SCR_005009 | 2026-02-17 10:00:45 | 16 | ||||||
|
PolySearch Resource Report Resource Website 10+ mentions |
PolySearch (RRID:SCR_005291) | PolySearch | data analysis service, production service resource, analysis service resource, service resource | A web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences. | text mining, disease, gene, protein, drug, metabolite, snp, gene sequence, pathway, tissue, gene family, subcellular localization, organ |
is listed by: OMICtools has parent organization: University of Alberta; Alberta; Canada |
OMICS_01194 | SCR_005291 | 2026-02-17 10:00:53 | 20 | |||||||||
|
SCAR Resource Report Resource Website 50+ mentions |
SCAR (RRID:SCR_006227) | SCAR | data analysis service, production service resource, analysis service resource, service resource | A web tool to create, display and manipulate structures of small molecules, proteins and DNA. | structure, small molecule, protein, dna, visualize, manipulate, display, create |
is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
nlx_151782 | SCR_006227 | Structure Creation and Representation, SCAR - Structure Creation and Representation, S.C.A.R., S.C.A.R | 2026-02-17 10:01:01 | 82 | ||||||||
|
SecStr Resource Report Resource Website 1+ mentions |
SecStr (RRID:SCR_006220) | SecStr | data analysis service, production service resource, analysis service resource, service resource | A tool to Predict the Secondary Structure of a protein from its amino acid sequence alone. The SecStr package uses six different secondary structure prediction methods (Nagano, Garnier et al., Burges et al., Chou and Fasman , Lim and Dufton and Hider). The results of those methods are combined into a Joint Prediction Histogram (JPH) as described by Hamodrakas, 1988 and Hamodrakas et al., 1982. As previously mentioned, the SecStr package contains computer programs making use of the secondary structure prediction methods of Nagano, Garnier et al., Burges et al., Chou and Fasman, Lim and Dufton and Hider. These programs were written in Fortran. The results of individual prediction methods are combined as described by Hamodrakas (1988), using a Perl program, to produce joint prediction histograms (JPH), for three types of secondary structure, which may be presented separately on a Java Applet. The output may be given either in text or graphics mode. For the latter a Java capable browser is required. | secondary structure, prediction, protein, algorithm, text, graphics |
is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
All rights are reserved for the whole or part of the program. Permission to use, Copy, And modify this software and its documentation is granted for academic use provided that:1. this copyright notice appears in all copies of the software and related documentation; 2. bugs will be reported to the authors. | nlx_151767 | SCR_006220 | SecStr - Secondary Structure Prediction, Secondary Structure Prediction, Secondary Structure Prediction of Proteins | 2026-02-17 10:00:47 | 7 | |||||||
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CW-PRED Resource Report Resource Website 10+ mentions |
CW-PRED (RRID:SCR_006188) | CW-PRED | data analysis service, production service resource, analysis service resource, service resource | A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif. | hidden markov model, gram-positive bacteria, protein, classification, cell-wall protein | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | Free for academic use, Acknowledgement requested | nlx_151733 | SCR_006188 | CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria | 2026-02-17 10:01:05 | 16 | |||||||
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orienTM Resource Report Resource Website |
orienTM (RRID:SCR_006218) | orienTM | data analysis service, production service resource, analysis service resource, service resource | A computer software that utilizes an initial definition of transmembrane segments to predict the topology of transmembrane proteins from their sequence. It uses position-specific statistical information for amino acid residues which belong to putative non-transmembrane segments derived from a statistical analysis of non-transmembrane regions of membrane proteins stored in the SwissProt database. Its accuracy compares well with that of other popular existing methods. | topology, prediction, transmembrane, protein, segment, algorithm, transmembrane protein |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
European Union ERBFMRXCT960019 | PMID:11477216 | nlx_151764 | SCR_006218 | orienTM - Orientation of TransMembrane proteins | 2026-02-17 10:01:01 | 0 | ||||||
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MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | data analysis service, production service resource, analysis service resource, service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-02-17 10:00:38 | 669 |
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