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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GARBAN Resource Report Resource Website |
GARBAN (RRID:SCR_005778) | GARBAN | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 12, 2012. GARBAN is a tool for analysis and rapid functional annotation of data arising from cDNA microarrays and proteomics techniques. GARBAN has been implemented with bioinformatic tools to rapidly compare, classify, and graphically represent multiple sets of data (genes/ESTs, or proteins), with the specific aim of facilitating the identification of molecular markers in pathological and pharmacological studies. GARBAN has links to the major genomic and proteomic databases (Ensembl, GeneBank, UniProt Knowledgebase, InterPro, etc.), and follows the criteria of the Gene Ontology Consortium (GO) for ontological classifications. Source may be shared: e-mail garban (at) ceit.es. Platform: Online tool | cdna microarray, proteomics, cdna, microarray, statistical analysis, gene, est, protein, genomic, gene ontology |
is listed by: Gene Ontology Tools is related to: Gene Ontology |
PMID:14594726 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149247 | http://garban.tecnun.es | SCR_005778 | Genomic Analysis and Rapid Biological ANnotation, University of Navarra; Pamplona; Spain | 2026-09-05 06:25:41 | 0 | |||||
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VectorBase Resource Report Resource Website 500+ mentions |
VectorBase (RRID:SCR_005917) | VectorBase | data or information resource, data repository, database, service resource, storage service resource | Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. | blast, clustalw, hmmer, vector, genomics, genome, sequence, population, insecticide resistance, annotation, microarray, gene expression, anatomy, pathogen, human, transcript, transcriptome, protein, proteome, mitochondria sequence, bioinformatics resource center, pathogen, arthropoda, vector control, ontology, software, source code, mitochondrial sequence, data analysis service, image collection, FASEB list |
is recommended by: National Library of Medicine is listed by: re3data.org is related to: Clustal W2 is related to: AnoBase: An Anopheles database is related to: Hmmer has parent organization: European Bioinformatics Institute has parent organization: University of Notre Dame; Indiana; USA |
European Union ; Evimalar network of excellence 242095; INFRAVEC 228421; NIAID |
PMID:22135296 PMID:19028744 PMID:18262474 PMID:18237287 PMID:17145709 |
Restricted | nif-0000-03624, r3d100010880 | https://doi.org/10.17616/R3CK6B | SCR_005917 | VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens, VectorBase, vector base | 2026-09-05 06:25:43 | 881 | ||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-09-05 06:25:42 | 7512 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-09-05 06:25:42 | 8 | |||||||
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ccPDB - Compilation and Creation of datasets from PDB Resource Report Resource Website 1+ mentions |
ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) | ccPDB | data access protocol, data or information resource, database, software resource, web service | ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible. | secondary structure, nucleic acid interaction, ligand interaction, structure, nucleic acid, interaction, ligand, data set, function, protein, annotate, tight-turn, nucleotide interacting residue, metals interacting residue, dna/rna binding residue, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Institute of Microbial Technology; Chandigarh; India |
OSDD ; DBT ; Council of Scientific and Industrial Research; New Delhi; India |
PMID:22139939 | biotools:ccpdb, nlx_149416 | https://bio.tools/ccpdb | SCR_005870 | Compilation and Creation of datasets from PDB, ccPDB - Compilation Creation of datasets from PDB | 2026-09-05 06:25:43 | 2 | |||||
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Newtomics Resource Report Resource Website 1+ mentions |
Newtomics (RRID:SCR_006073) | Newt-Omics | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169 | gene expression, regeneration, annotation, expression data, peptide sequence, gene sequence, tissue regeneration, newt, pathway, mammal, blast, contigs, peptide, tissue, microarray, heart, lens, dorsal, ventral, transcript, functional annotation, molecular process, model organism, expressed sequence tag, sequence, mass spectrometry, protein, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute for Heart and Lung Research; Bad Nauheim; Germany |
Hessian Ministry for Science and Art | PMID:22039101 | To be used only for research and educational purposes. Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the MPI for heart and lung research. | nlx_151479, biotools:newt-omics | https://bio.tools/newt-omics | SCR_006073 | newt db, Newt database | 2026-09-05 06:25:46 | 1 | ||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-09-05 06:25:46 | 25 | ||||
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LepChorionDB Resource Report Resource Website |
LepChorionDB (RRID:SCR_006222) | LepChorionDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A relational database of Lepidoptera chorion proteins. The proteinaceous Lepidopteran chorions are used in our lab, as a model system towards unraveling the routes and rules of formation of natural protective amyloids. Therefore, we constructed LepChorionDB a relational database, containing all Lepidoptera chorion proteins identified to date. Lepidoptera chorion proteins can be classified in two major protein families, A and B. This classification was based on multiple sequence alignments of conserved key residues, in the central domain of, well characterized, silkmoth chorion proteins. These alignments were used to build Hidden Markov Models in order to search various DataBases. This work was a collaboration of the Department of Cell Biology and Biophysics, University of Athens and the Centre of Immunology & Transplantation Biomedical Research Foundation, Academy of Athens. | lepidoptera, chorion, protein, proteome, silkmoth, insect | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | nlx_151769 | SCR_006222 | Lepidoptera chorion protein database, LepChorionDB - Lepidoptera chorion protein database | 2026-09-05 06:25:49 | 0 | ||||||||
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OMPdb Resource Report Resource Website |
OMPdb (RRID:SCR_006221) | OMPdb | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database of Beta-barrel outer membrane proteins from Gram-negative bacteria. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database''s protein entries or run BLAST searches against the database. The most up-to-date version of the database (as well as all past versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences). For constructing OMPdb, multiple freely accessible resources were combined and a detailed literature search was performed. The classification of OMPdb''s protein entries into families is based mainly on structural and functional criteria. Information included in the database consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for Beta-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel Beta-barrel proteins and whole-genome analyses., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | beta-barrel, outer membrane protein, gram-negative bacteria, protein, protein sequence, transmembrane, annotation, genome-wide analyses, comparative genomics, sequence, structure, blast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20952406 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01611, biotools:ompdb, nlx_151768 | https://bio.tools/ompdb | SCR_006221 | OMPdb - A database of Beta-barrel outer membrane proteins from Gram-negative bacteria | 2026-09-05 06:25:49 | 0 | |||||
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University of Athens Biophysics and Bioinformatics Laboratory Resource Report Resource Website 1+ mentions |
University of Athens Biophysics and Bioinformatics Laboratory (RRID:SCR_006180) | University of Athens Biophysics & Bioinformatics Laboratory | data or information resource, degree granting program, graduate program resource, laboratory portal, organization portal, portal, training resource, undergraduate program resource | Laboratory focuses on research related to the elucidation of the principles governing protein structure and function, under the supervision of Professor Stavros J. Hamodrakas. In particular, original research is carried out along two main axes: # Algorithm development for the prediction of protein structure, function and interactions from amino acid sequence as well as construction of relevant databases. # Application of a variety of Biophysical methods and techniques for protein structure determination and for structural studies of complex, physiologically important, Biological tissues such as insect chorion and cuticle. More than 15 individuals (including post-doctoral researchers, PhD students, MSc and undergraduate students) are currently involved in several ongoing research projects. Apart from research, our lab offers undergraduate courses in Bioinformatics and Molecular Biophysics, which are elective for the degrees (BSc) in Biology (Faculty of Biology) and Physics (Faculty of Physics) of the University of Athens. At the same time, our lab is actively involved in the organization and co-ordination of the MSc Programme in Bioinformatics of the Faculty of Biology. | biophysics, bioinformatics, protein structure, protein function, protein, protein interaction, amino acid sequence, algorithm, prediction, structure, function, interaction |
has parent organization: University of Athens; Athens; Greece is parent organization of: PredSL is parent organization of: CAST is parent organization of: PRED-SIGNAL is parent organization of: AMYL-PRED is parent organization of: HMM-TM is parent organization of: PRED-LIPO is parent organization of: CW-PRED is parent organization of: PRED-TMBB is parent organization of: PRED-COUPLE 2 is parent organization of: ConBBPRED is parent organization of: PRED-GPCR is parent organization of: MCMBB is parent organization of: waveTM is parent organization of: PRED-TMR is parent organization of: GeneVito is parent organization of: PRED-CLASS is parent organization of: CoPreTHi is parent organization of: orienTM is parent organization of: SecStr is parent organization of: OMPdb is parent organization of: LepChorionDB is parent organization of: Human-gpDB is parent organization of: hPATM is parent organization of: NON-RED is parent organization of: DAM-Bio is parent organization of: SCAR is parent organization of: FT is parent organization of: DnaProt is parent organization of: CuticleDB is parent organization of: gpDB - a database of GPCRs G-proteins Effectors and their interactions is parent organization of: TMRPres2D is parent organization of: ExTopoDB |
nlx_151727 | SCR_006180 | Biophysics and Bioinformatics Laboratory at University of Athens, Biophysics and Bioinformatics Laboratory of the Department of Cell Biology and Biophysics of the University of Athens | 2026-09-05 06:25:48 | 2 | ||||||||
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SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SitEx Database | 2026-09-05 06:25:47 | 1 | ||||
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PSCDB - Protein Structural Change DataBase Resource Report Resource Website |
PSCDB - Protein Structural Change DataBase (RRID:SCR_006116) | PSCDB | data or information resource, database, image collection | Database for protein structural change upon ligand binding that are classified into 7 classes in terms of the ligand binding sites and the location where the dominant motion occurs. # Coupled Domain motions are the domain motions induced upon ligand binding. # Independent Domain motions are the observable domain motions regardless of ligand binding. # Coupled Local motions are the local motions induced upon ligand binding. # Independent Local motions are the observable local motions regardless of ligand binding. # Burying ligand motions are imaginable motions required to hold ligand protein-inside. # No significant motions mean just nothing happen. # Other motions are motions unclassified into domain and local motions. Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. | protein, structure, ligand binding, ligand-free, ligand-bound, monomeric protein, homo-dimeric protein, animation, ligand, structural change | has parent organization: Nagoya University; Nagoya; Japan | Japanese Ministry of Education Culture Sports Science and Technology MEXT 20370063; Japanese Ministry of Education Culture Sports Science and Technology MEXT 21107523 |
PMID:22080505 PMID:21376729 |
nlx_151591 | SCR_006116 | Protein Structural Change DataBase (PSCDB), Protein Structural Change DataBase | 2026-09-05 06:25:47 | 0 | ||||||
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Proteome Commons Resource Report Resource Website 10+ mentions |
Proteome Commons (RRID:SCR_006234) | Proteome Commons | community building portal, data or information resource, data repository, database, portal, service resource, software resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A public resource for sharing general proteomics information including data (Tranche repository), tools, and news. Joining or creating a group/project provides tools and standards for collaboration, project management, data annotation, permissions, permanent storage, and publication. | proteomics, protein, peptide, data sharing, data, tool, news, annotation, proteome, genome |
is listed by: re3data.org has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: Proteome Commons Tranche repository |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:20356086 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151800 | SCR_006234 | ProteomeCommons.org, ProteomeCommons | 2026-09-05 06:25:49 | 12 | |||||
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I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-09-05 06:24:56 | 23 | ||||
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Human Proteinpedia Resource Report Resource Website 10+ mentions |
Human Proteinpedia (RRID:SCR_002948) | Human Proteinpedia | data or information resource, data repository, database, service resource, storage service resource | A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted. | enzyme, protein expression, post-translational modification, protein-protein interaction, subcellular localization, enzyme substrate, tissue expression, protein, protein binding, peptide, mass spectrometry, mass spectrometry spectra, immunohistochemistry, western blotting, microarray, co-immunoprecipitation, fluorescence, annotation, cell line expression, disease tissue expression, FASEB list |
is listed by: re3data.org is related to: HPRD - Human Protein Reference Database has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18259167 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02999, r3d100010985 | https://doi.org/10.17616/R3V62C | SCR_002948 | 2026-09-05 06:24:56 | 32 | ||||||
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Computational Biology Center Resource Report Resource Website 50+ mentions |
Computational Biology Center (RRID:SCR_002877) | data or information resource, disease-related portal, portal, topical portal, training resource | Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling | drug, evolution, experiment, gene, algorithm, bioinformatics, biology, cancer, clinical, computational, diagnostic, genome, human, initiation, kinetics, laboratory, leukemia, ligand, metastasis, microrna, mirna, model, molecular, network, pathway, phenotype, prognostic, progression, protein, regulation, research, resistance, rna, sequence, stem cell, structure, t cell, therapy, treatment, tumor | is parent organization of: TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences | Free, Freely available | nif-0000-25560 | SCR_002877 | cBio | 2026-09-05 06:24:54 | 71 | ||||||||
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Tuschl Laboratory: RNA Molecular Biology Resource Report Resource Website 1+ mentions |
Tuschl Laboratory: RNA Molecular Biology (RRID:SCR_002866) | data or information resource, laboratory portal, organization portal, portal | RNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes. | genetics, biochemical, biology, catalyst, mechanism, mirna, molecule, process., protein, regulation, rna, sequence, sirna, technique | has parent organization: Rockefeller University; New York; USA | Free, Freely available | nif-0000-25546 | http://www.rockefeller.edu/labheads/tuschl/sirna.html | SCR_002866 | Tuschl Lbaoratory | 2026-09-05 06:24:54 | 5 | |||||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/, https://bio.tools/dialign-tx | https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-09-05 06:24:57 | 44 | ||||
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SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-09-05 06:24:59 | 1307 | |||||
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PredictNLS Resource Report Resource Website 10+ mentions |
PredictNLS (RRID:SCR_003133) | PredictNLS | analysis service resource, data analysis service, production service resource, service resource, software resource | Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given. | bio.tools, nuclear localization signal, protein, protein sequence |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ROSTLAB has parent organization: Columbia University; New York; USA |
DOI:10.1093/embo-reports/kvd092 | Free, Available for download, Freely available | nif-0000-31416, OMICS_01633, SCR_008553, biotools:predictnls | https://www.rdocumentation.org/packages/propagate/versions/1.0-4/topics/predictNLS | SCR_003133 | Prediction and Analysis of Nuclear Localization Signals | 2026-09-05 06:24:58 | 33 |
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