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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SPOT - Biological prioritization after a SNP association study Resource Report Resource Website 500+ mentions |
SPOT - Biological prioritization after a SNP association study (RRID:SCR_005193) | SPOT | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for using biological databases to prioritize single nucleotide polymorphisms (SNPs) after a genome-wide association study (GWAS). The site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. Users can specify candidate genes or genomic regions with custom levels of prioritization. The results can be downloaded or viewed in the browser where users can interactively explore the details of each SNP, including graphical representations of the genomic information network (GIN) method. For investigators interested in incorporating biological databases into a post-GWAS SNP selection strategy, the SPOT web tool is an easily implemented and flexible solution. | single nucleotide polymorphism, genome-wide association study, linkage disequilibrium, gene, genomic region, p-value, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:20529875 | biotools:spot, OMICS_00189 | https://bio.tools/spot | SCR_005193 | 2026-09-19 12:56:49 | 512 | |||||||
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MG-RAST Resource Report Resource Website 1000+ mentions |
MG-RAST (RRID:SCR_004814) | MG RAST | analysis service resource, data analysis service, production service resource, service resource | An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. | metagenome, base pair, sequence, phylogenetic, functional analysis, data sharing, metadata, protein, micro biome, analysis platform, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: Argonne National Laboratory |
NIAID contract HHSN272200900040C; DOE contract DE-AC02-06CH11357 |
PMID:18803844 | Acknowledgement requested, Public, Account required | OMICS_01456, biotools:mg-rast | http://metagenomics.nmpdr.org, https://bio.tools/mg-rast | SCR_004814 | The Metagenomics RAST server, Metagenomics RAST, MG-RAST - metagenomics analysis server | 2026-09-19 12:56:47 | 1165 | ||||
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GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | data or information resource, database, service resource | An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. | functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Set Enrichment Analysis is related to: MapMan is related to: Biomine is related to: SEGS has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
Slovenian Research Agency J4-2228; Slovenian Research Agency P2-0103 |
PMID:24194592 | Creative Commons Attribution-NonCommercial-ShareAlike License | biotools:gomapman, OMICS_02280 | https://bio.tools/gomapman | SCR_005060 | 2026-09-19 12:56:48 | 29 | |||||
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Human Splicing Finder Resource Report Resource Website 1000+ mentions |
Human Splicing Finder (RRID:SCR_005181) | HSF | analysis service resource, data analysis service, production service resource, service resource | Software tool to help study pre-mRNA splicing and to better understand intronic and exonic mutations leading to splicing defects. To calculate the consensus values of potential splice sites and search for branch points, new algorithms were developed. Furthermore, they have integrated all available matrices to identify exonic and intronic motifs, as well as new matrices to identify hnRNP A1, Tra2-? and 9G8. | splicing, mutation, splicing signal, sequence, transcript, nucleotide, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Ensembl has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:19339519 | Acknowledgement requested | biotools:human_splicing_finder, OMICS_00176 | https://bio.tools/human_splicing_finder | http://www.umd.be/HSF/ | SCR_005181 | 2026-09-19 12:56:49 | 1009 | |||||
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Apo and Holo structures DataBase Resource Report Resource Website 1+ mentions |
Apo and Holo structures DataBase (RRID:SCR_004800) | AH-DB | data or information resource, database | Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms. | ah-db, ahdb, apo, holo, protein interaction, structural change, protein, protein structure, protein binding, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Cheng Kung University; Tainan; Taiwan |
National Science Council Taiwan NSC 99-2628-E-006-017 | PMID:22084200 | The community can contribute to this resource | biotools:ah-db, nlx_143908 | https://bio.tools/ah-db | SCR_004800 | Apo-Holo DataBase | 2026-09-19 12:56:47 | 1 | ||||
|
NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj, https://bio.tools/bioproject, https://doi.org/10.17616/R31NJMS2 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | NCBI BioProject Database, BioProject | 2026-09-19 12:56:47 | 14025 | ||||
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StSNP Resource Report Resource Website 1+ mentions |
StSNP (RRID:SCR_005417) | StSNP | analysis service resource, data analysis service, production service resource, service resource | A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00138, biotools:stsnp | https://bio.tools/stsnp | SCR_005417 | Structure SNP | 2026-09-19 12:56:51 | 3 | |||||||
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PRINSEQ Resource Report Resource Website 1000+ mentions |
PRINSEQ (RRID:SCR_005454) | PRINSEQ | analysis service resource, data analysis service, production service resource, service resource | A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, data analysis, genomic sequence data, metagenomic sequence data, summary, perl, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools has parent organization: San Diego State University; California; USA |
PMID:21278185 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01068, biotools:prinseq | http://prinseq.sourceforge.net, https://bio.tools/prinseq | SCR_005454 | PReprocessing and INformation of SEQuences, preprocessing and information of sequences | 2026-09-19 12:56:51 | 1199 | |||||
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TMA Navigator Resource Report Resource Website 1+ mentions |
TMA Navigator (RRID:SCR_005599) | TMA Navigator | analysis service resource, data analysis service, production service resource, service resource | A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement. | tissue microarray, network, analysis, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23761446 | Acknowledgement requested, Free | biotools:tma_navigator, OMICS_00821 | https://bio.tools/tma_navigator | SCR_005599 | 2026-09-19 12:56:52 | 5 | ||||||
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MethylomeDB Resource Report Resource Website 1+ mentions |
MethylomeDB (RRID:SCR_005583) | MethylomeDB | data or information resource, database | A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database. | brain, dna methylation, dorsal lateral prefrontal cortex, ventral prefrontal cortex, auditory cortex, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Columbia University; New York; USA |
NIH ; NHGRI HG002915; NIMH MH074118 |
PMID:22140101 | OMICS_01843, biotools:methylomedb, nlx_146210 | https://bio.tools/methylomedb | SCR_005583 | MethylomeDB - the Brain Methylome Database, Brain Methylome Database | 2026-09-19 12:56:52 | 1 | |||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-09-19 12:56:53 | 36 | |||||
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MIPModDB Resource Report Resource Website 1+ mentions |
MIPModDB (RRID:SCR_006058) | MIPModDB | data or information resource, database | This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database. | major intrinsic protein, model, protein structure, structural model, sequence, structure, superfamily, genome sequence, amino acid sequence, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Indian Institute of Technology Kanpur; Uttar Pradesh; India |
Government of India | PMID:22080560 | Free | nlx_151460, biotools:mipmoddb | https://bio.tools/mipmoddb | SCR_006058 | Major Intrinsic Protein superfamily Models, MIPModDB - Major Intrinsic Protein superfamily Models | 2026-09-19 12:56:55 | 6 | ||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | analysis service resource, data analysis service, production service resource, service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-09-19 12:56:54 | 398 | ||||
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RecountDB Resource Report Resource Website |
RecountDB (RRID:SCR_006117) | RecountDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database for corrected read counts and genome mapping on NCBI's Short Read Archive. The corrected count was done using RECOUNT and the mapping with LAST. We also provide information of reference genome to which we aligned the short reads. We focus on transcriptomic data, specifically TSS-Seq and RNA-Seq. Because this is the type of data for which sequence count correction is most important. Hence we do not include the genomic reads. The current version contains 2,265 entries from 45 organisms, with read lengths from 17 to 100bp. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. We provide the data grouped according to the genome, type of studies and submitter in TAB , PSL and BAM format. They contain the mapping position and annotation of reads observed and corrected counts. | read count, genome mapping, short read, genome, transcript, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: NCBI Sequence Read Archive (SRA) is related to: RECOUNT is related to: LAST has parent organization: National Institute of Advanced Industrial Science and Technology |
Japanese Ministry of Education Culture Sports Science and Technology MEXT 221S002 | PMID:22139942 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151592, biotools:recountdb | https://bio.tools/recountdb | SCR_006117 | 2026-09-19 12:56:56 | 0 | |||||
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SNPsandGO Resource Report Resource Website 50+ mentions |
SNPsandGO (RRID:SCR_005788) | SNPs&GO | analysis service resource, data analysis service, production service resource, service resource | A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans. | prediction, protein, mutation, disease, single nucleotide polymorphism, bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Bologna; Bologna; Italy |
PMID:19514061 | biotools:snps_go, OMICS_02219 | https://bio.tools/snps_go | SCR_005788 | SNPs and GO | 2026-09-19 12:56:53 | 61 | ||||||
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ProRepeat Resource Report Resource Website 1+ mentions |
ProRepeat (RRID:SCR_006113) | ProRepeat | data or information resource, database | ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats' corresponding codons. | amino acid, tandem, repeat, protein, sequence, nucleotide sequence, repeat fragment, protein repeat, proteome, sequence length, gene, taxon, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: UniProtKB is related to: RefSeq has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
PMID:22102581 | nlx_151587, biotools:prorepeat | https://bio.tools/prorepeat | SCR_006113 | 2026-09-19 12:56:56 | 1 | |||||||
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ProtChemSI Resource Report Resource Website 1+ mentions |
ProtChemSI (RRID:SCR_006115) | ProtChemSI | data or information resource, database | The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly. | protein, chemical, 3d structure, biological network, interaction, ligand, prediction, fasta, fasta sequence, smiles string, complex, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Heidelberg University; Baden-Wurttemberg; Germany |
PMID:21573205 | Acknowledgement requested | nlx_151590, biotools:protchemsi | https://bio.tools/protchemsi | SCR_006115 | Protein-Chemical Structural Interactions, ProtChemSI: protein-chemical interaction database, ProtChemSI - the database of protein-chemical structural interactions | 2026-09-19 12:56:56 | 3 | |||||
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Yeast Search for Transcriptional Regulators And Consensus Tracking Resource Report Resource Website 100+ mentions |
Yeast Search for Transcriptional Regulators And Consensus Tracking (RRID:SCR_006076) | YEASTRACT | data or information resource, database | A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database. | yeast, gene, regulatory association, transcription factor, target gene, genomic, transcription regulation, transcription, web service, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SGD is related to: Gene Ontology is related to: Regulatory Sequence Analysis Tools |
Fundacao para a Ciencia e a Tecnologia contract Pest-OE/EQB/LA0023/2011_research line: Systems and Synthetic Biology; Fundacao para a Ciencia e a Tecnologia ERA-IB/0002/2010; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-EIA/111239/2009; Fundacao para a Ciencia e a Tecnologia PTDC/EIA-CCO/118522/2010 |
PMID:24170807 PMID:20972212 PMID:18032429 PMID:16381908 |
Free | nif-0000-03652, OMICS_00547, biotools:yeastract | https://bio.tools/yeastract | SCR_006076 | 2026-09-19 12:56:55 | 130 | |||||
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HotRegion - A Database of Cooperative Hotspots Resource Report Resource Website 1+ mentions |
HotRegion - A Database of Cooperative Hotspots (RRID:SCR_006022) | HotRegion | data or information resource, database | Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. HotRegion provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. The number of interfaces in the database is 147909 and still growing. | residue, chain, complex, monomer, pair potential, hotspot, hotregion, accessible surface area, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Koc University; Istanbul; Turkey |
Turkish Academy of Sciences ; TUBITAK 109T343; TUBITAK 109E207 |
PMID:22080558 | nlx_151420, biotools:hotregion | https://bio.tools/hotregion | SCR_006022 | HotRegion: a database of predicted hot spot clusters, HotRegion: A database of cooperative hot spots | 2026-09-19 12:56:55 | 5 | |||||
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glycomedb Resource Report Resource Website 10+ mentions |
glycomedb (RRID:SCR_005717) | GlycomeDB | data or information resource, database | GlycomeDB is a database of all known carbohydrate structures. This was achieved by crosslinking several other databases of carbohydrate structures by using the GlycoCT XML language specification. We have analyzed all of the existing public databases and defined a sequence format based on XML (GlycoCT) capable of storing all structural information of carbohydrate sequences. We have implemented a library of parsers for the interpretation of the different encoding schemes for carbohydrates. With this library we have translated the carbohydrate sequences of all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank) to GlycoCT, and created a new database (GlycomeDB) containing all structures and annotations. During the process of data integration we found multiple inconsistencies in the existing databases which were corrected in collaboration with the responsible curators. With the new database, GlycomeDB, it is possible to get an overview of all carbohydrate structures in the different databases and to crosslink common structures in the different databases. Scientists are now able to search for a particular structure in the meta database and get information about the occurrence of this structure in the five carbohydrate structure databases. | carbohydrate structure, carbohydrate, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: German Cancer Research Center |
European Union FP6 ; DFG |
PMID:21045056 PMID:19759275 PMID:18803830 |
nlx_149174, r3d100011527, biotools:glycomedb | https://bio.tools/glycomedb, https://doi.org/10.17616/R34M07 | SCR_005717 | GlycomeDB - A carbohydrate structure metadatabase | 2026-09-19 12:56:53 | 25 |
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