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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PRED-TMR2 Resource Report Resource Website 1+ mentions |
PRED-TMR2 (RRID:SCR_006205) | PRED-TMR2 | service resource, analysis service resource, data analysis service, production service resource | A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2. | prediction, transmembrane, protein, algorithm, neural network, classification, transmembrane protein, protein classification, membrane protein, protein structure |
is related to: DAM-Bio has parent organization: PRED-TMR |
European Union ERBFMRXCT960019 | PMID:10469822 | nlx_151766 | SCR_006205 | PRED-TMR2: Prediction of Transmembrane regions in proteins | 2026-08-11 09:41:22 | 1 | ||||||
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Subcellular Location Image Finder Resource Report Resource Website 1+ mentions |
Subcellular Location Image Finder (RRID:SCR_006723) | SLIF | data or information resource, database, image | SLIF finds fluorescence microscope images in on-line journal articles, and indexes them according to cell line, proteins visualized, and resolution. Images can be accessed via the SLIF Web database. SLIF takes on-line papers and scans them for figures that contain fluorescence microscope images (FMIs). Figures typically contain multiple FMIs, to SLIF must segment these images into individual FMIs. When the FMI images are extracted, annotations for the images (for instance, names of proteins and cell-lines) are also extracted from the accompanying caption text. Protein annotation are also used to link to external databases, such as the Gene Ontology DB. The more detailed process includes: segmentation of images into panels; panel classification, to find FMIs; segmentation of the caption, to find which portions of the caption apply to which panels; text-based entity extraction; matching of extracted entities to database entries; extraction of panel labels from text and figures; and alignment of the text segments to the panels. Extracted FMIs are processed to find subcellular location features (SLFs), and the resulting analyzed, annotated figures are stored in a database, which is accessible via SQL queries. | fluorescence, annotation, cell, journal, microscope, protein, subcellular, image, cell line, fluorescence microscope, information retrieval, data mining |
is listed by: Biositemaps has parent organization: Carnegie Mellon University; Pennsylvania; USA |
Commonwealth of Pennsylvania Tobacco Settlement Fund ; National Center for Integrative Biomedical Informatics ; NIGMS R01 GM078622; NIDA U54 DA021519 |
PMID:17990497 | nif-0000-10308 | SCR_006723 | SLIF - Subcellular Location Image Finder | 2026-08-11 09:41:23 | 1 | ||||||
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Musculoskeletal Transplant Foundation - MTF Resource Report Resource Website 1+ mentions |
Musculoskeletal Transplant Foundation - MTF (RRID:SCR_006684) | MTF | biomaterial supply resource, tissue bank, material resource | The Musculoskeletal Transplant Foundation is a non-profit service organization dedicated to providing quality allograft tissue through a commitment to excellence in education, research, recovery and care for recipients, donors and their families. We are a national consortium comprised of academic medical institutions, organ procurement organizations and tissue recovery organizations. MTF was created as a charitable organization with a mission that is dedicated to the needs of donors, donor families, patients and surgeons. We focus on respectful stewardship of the donated gift while advancing the science and practice of bone, ligament, cartilage and skin transplantation. Since our inception in 1987, MTF has recovered more than 60,000 donors and distributed more than 3 million grafts for transplantation. We also support research to expand the science of transplantation, and we encourage the efforts of our members and non-member clients to improve the understanding of donation and transplantation among the medical community and the public at large. Our policies are developed and implemented by MTF''''s Medical Board of Trustees, Donation Board of Trustees and Board of Directors, composed of physicians and recovery agency representatives who are dedicated to the mission of the Foundation. This fundamental commitment enables us to set and maintain the highest levels of safety assurance and quality control in all phases of our operations. |
is listed by: One Mind Biospecimen Bank Listing is parent organization of: International Institute for the Advancement of Medicine |
nlx_89982 | SCR_006684 | Musculoskeletal Transplant Foundation | 2026-08-11 09:41:23 | 1 | |||||||||
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Lists2Networks Resource Report Resource Website 1+ mentions |
Lists2Networks (RRID:SCR_006323) | L2N | service resource, analysis service resource, data analysis service, production service resource | A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. | high-throughput sequencing, analysis, gene, protein |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20152038 | Free, Public, Account required | OMICS_02231 | http://www.lists2networks.org | SCR_006323 | Lists2Networks: Integrated analysis of gene/protein lists | 2026-08-11 09:41:19 | 3 | |||||
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PRED-TMR Resource Report Resource Website 1+ mentions |
PRED-TMR (RRID:SCR_006203) | PRED-TMR | service resource, analysis service resource, data analysis service, production service resource | A web server that predicts transmembrane domains in proteins using solely information contained in the sequence itself. The algorithm refines a standard hydrophobicity analysis with a detection of potential termini (edges, starts and ends) of transmembrane regions. This allows both to discard highly hydrophobic regions not delimited by clear start and end configurations and to confirm putative transmembrane segments not distinguishable by their hydrophobic composition. The accuracy obtained on a test set of 101 non homologous transmembranes proteins with reliable topologies compares well with that of other popular existing methods. Only a slight decrease in prediction accuracy was observed when the algorithm was applied to all transmembrane proteins of the SwissProt database (release 35). | predict, transmembrane segment, protein, algorithm, sequence, membrane protein, protein structure, transmembrane region, hydrophobicity analysis |
is related to: waveTM is related to: DAM-Bio has parent organization: University of Athens Biophysics and Bioinformatics Laboratory is parent organization of: PRED-TMR2 |
European Union ERBFMRXCT960019 | PMID:10360978 | nlx_151765 | SCR_006203 | PRED-TMR: A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database | 2026-08-11 09:41:17 | 7 | ||||||
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KI Biobank - Tissue Biobank Resource Report Resource Website 1+ mentions |
KI Biobank - Tissue Biobank (RRID:SCR_006043) | KI Biobank - Tissue Biobank | biomaterial supply resource, tissue bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 4, 2014. Tissue Biobank collects samples from different types of cancers patients prospectively. Blood samples are being sent to KI Biobank for DNA extraction and storage. Number of sample donors: 611 (June 2010) | blood, dna |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Karolisnka Biobank |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151440 | SCR_006043 | 2026-08-11 09:41:15 | 1 | |||||||
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Phenomizer Resource Report Resource Website 10+ mentions |
Phenomizer (RRID:SCR_006157) | service resource, production service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 31,2026. Phenomizer offers three different approaches to find the appropriate term for a phenotypic abnormality, indicated by the three tabs on the left hand side: Feature, Disease and Ontology. The Phenomizer is intended to be used by qualified and licensed physicians in order to provide assistance in reaching the correct diagnosis in patients with hereditary diseases and for use as a teaching aid. The Phenomizer does not make diagnoses. Rather, it produces a ranked list of possibilities that can be used by physicians as a part of the diagnostic workup. The Phenomizer does not contain information about all possible diagnoses or even all possible hereditary diseases. The Phenomizer should not be used to make medical decisions without the advice of a physician. | feature, disease, ontology, clinical, differential diagnoses |
is related to: Human Phenotype Ontology is related to: Human Phenotype Ontology has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19800049 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151657 | SCR_006157 | Phenomizer - Clinical Diagnostics with Similarity Searches in Ontologies | 2026-08-11 09:41:17 | 32 | |||||||
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Aggrescan: The Hot Spot Finder Resource Report Resource Website 50+ mentions |
Aggrescan: The Hot Spot Finder (RRID:SCR_008403) | Aggrescan | service resource, analysis service resource, data analysis service, production service resource | Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies. | aggregation, amino acid, protein, mutation, polypeptide, amyloid, bacterial protein, protein aggregation, neurodegeneration |
is listed by: 3DVC has parent organization: Autonomous University of Barcelona; Barcelona; Spain |
Ministerio de Educacion y Ciencia BIO2004-05879; Ministerio de Educacion y Ciencia BIO2003-02848; Spain Generalitat de Catalunya SGR2005-00037; Spain Generalitat de Catalunya SGR2005-01037 |
PMID:17324296 | Free, Acknowledgement requested | nif-0000-30073 | SCR_008403 | 2026-08-11 09:41:42 | 65 | ||||||
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Danubian Biobank Consortium Resource Report Resource Website 1+ mentions |
Danubian Biobank Consortium (RRID:SCR_010566) | biomaterial supply resource, tissue bank, material resource | Not yet vetted by NIF curator | nlx_39960 | SCR_010566 | 2026-08-11 09:42:11 | 1 | ||||||||||||
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RTI Biologics Resource Report Resource Website 1+ mentions |
RTI Biologics (RRID:SCR_010721) | RTI | biomaterial supply resource, tissue bank, material resource | Provides sterile biologic implants of human bone and tissues used in spine, sports medicine, orthopedic, dental and other specialty surgeries. | is listed by: One Mind Biospecimen Bank Listing | nlx_97050 | SCR_010721 | RTI Biologics Inc, RTI Biologics Inc. | 2026-08-11 09:42:13 | 1 | |||||||||
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Alpha Genesis Resource Report Resource Website 50+ mentions |
Alpha Genesis (RRID:SCR_010568) | AGI | biomaterial supply resource, tissue bank, material resource | A company which provides nonhuman primate products and bio-research services for the global scientific community. They provide serum, plasma, whole blood, and tissue samples from primates such as the Cynomolgus macaque, the Rhesus macaque, and the African Green. Products based on others species are available upon request. | commercial, supplier, nonhuman primate, macaque, african green | Commercial | nlx_40671 | http://www.alphagenesisinc.com/bioproducts.html | SCR_010568 | Alpha Genesis Inc, Alpha Genesis Incorporated | 2026-08-11 09:42:15 | 56 | |||||||
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NCI National Products Branch Resource Report Resource Website 100+ mentions |
NCI National Products Branch (RRID:SCR_010603) | biomaterial supply resource, tissue bank, material resource | Not yet vetted by NIF curator | nlx_51144 | SCR_010603 | 2026-08-11 09:42:11 | 100 | ||||||||||||
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Statistical Torsional Angles Potentials of NMR Refinement Database Resource Report Resource Website 1+ mentions |
Statistical Torsional Angles Potentials of NMR Refinement Database (RRID:SCR_008917) | STAP of NMR Refinement Database | data or information resource, database, image | STAP refinement of NMR Database is based the Statistical Torsion Angles Potentials to refine the NMR structure. It stored original solution NMR structures from the Protein Data Banks and our refined structures. Currently we carried out 2,405 refined NMR structure (until Sept 20, 2011). According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. STAP of NMR Refinement Database is a public database of 2405 refined NMR solution structures from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analyzed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, (1)-(2) rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research. | nmr structure, statistical, torsion angle, potential, nuclear magnetic resonance, structure, ramachandran |
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea |
Korean Ministry of Education Science and Technology 20110002321; Korean Ministry of Education Science and Technology 20110019747 |
PMID:22102572 | Public | nlx_151605 | SCR_008917 | STAP refinement of NMR DB, STAP - NMR Refinement Database, STAP refinement of NMR Database | 2026-08-11 09:41:49 | 3 | |||||
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Rhesus Monkey Breeding and Research Resource Report Resource Website 1+ mentions |
Rhesus Monkey Breeding and Research (RRID:SCR_008357) | RMBRR | biomaterial supply resource, tissue bank, material resource | This colony provides a national resource of rhesus monkeys and their tissues to carry out research benefiting the scientific community. The RMBRR maintains a colony of monkeys that have been derived to be specific pathogen free for members of both the herpes and retrovirus families. Over its history, the RMBRR has developed specialized management techniques, housing facilities and highly trained staff to avail these purposefully bred laboratory models, which are 93% genetically identical to humans, to researchers worldwide. Historically, this animal model has been instrumental in research involving blood classification, polio vaccine development, and drug safety and efficacy while currently they are the preferred model for studying the mechanisms of immunodeficiency diseases. Their susceptibility to Simian Immunodeficiency Virus and their homology to the human major histocompatibility complex (MHC) Class I, II and TCR genes make them valuable in HIV research. They are currently the models of choice for HIV/AIDS vaccine development and study. Other areas of research include atherosclerosis, myocarditis, alcoholism, diabetes, cancer and aging. The overall objectives of this resource are to improve the resources available at the RMBRR and to conduct resource-relevant research that improves both the health of the rhesus colony and its usefulness for studies of human disease. The Resource and Management Core is responsible for providing animal resources, tissues/biological fluids, cell lines, expert advice and research support to NIH extramural and intramural programs, other federal agencies and to private sponsors. The Resource-Related Research Core conducts research to improve the health of the animals maintained with special emphasis on studies that will enhance the usefulness of the rhesus as a model for studies of human disease. | animal model, tissue, live animal, cell line, bodily fluid, vaccine development, vaccine |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Texas MD Anderson Cancer Center |
Immunodeficiency disease, Human immunodeficiency virus, AIDS, Atherosclerosis, Myocarditis, Alcoholism, Diabetes, Cancer, Aging | Public: available to researchers worldwide | nif-0000-25893 | SCR_008357 | KCCMR Rhesus Monkey Breeding and Research, KCCMR RMBRR, Keeling Center for Comparative Medicine and Research Rhesus Monkey Breeding and Research | 2026-08-11 09:41:40 | 1 | ||||||
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Singapore Tissue Network Resource Report Resource Website 1+ mentions |
Singapore Tissue Network (RRID:SCR_010697) | biomaterial supply resource, tissue bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_81651 | http://www.stn.org.sg/ | SCR_010697 | 2026-08-11 09:42:07 | 1 | ||||||||||
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OHSU Animal Model Support Core Facility Resource Report Resource Website 1+ mentions |
OHSU Animal Model Support Core Facility (RRID:SCR_009994) | OHSU TMM, TMM Core | service resource, core facility, access service resource | Core assists investigators with developing genetically engineered rodent models of human diseases for studying mutant genes and investigating molecular mechanisms underlying pathological processes. | ABRF, USEDit, developing genetically engineered rodent models, human diseases, mutant genes, pathological processes |
is listed by: Eagle I is related to: USEDit has parent organization: Oregon Health and Science University; Oregon; USA |
SciEx_9275, SCR_011002, nlx_156461 | http://ohsu.eagle-i.net/i/0000012a-2501-9822-d994-629180000000, http://www.scienceexchange.com/facilities/transgenic-mouse-models-ohsu | SCR_009994 | OHSU Transgenic Mouse Models Core Laboratory, Oregon Health & Science University Transgenic Mouse Models, Oregon Health and Science University Transgenic Mouse Models, OHSU Transgenic Mouse Model Shared Resource | 2026-08-11 09:42:06 | 2 | |||||||
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NEBcutter Resource Report Resource Website 100+ mentions |
NEBcutter (RRID:SCR_010664) | service resource, analysis service resource, data analysis service, production service resource | This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: New England Biolabs |
PMID:12824395 | biotools:nebcutter, nlx_71778 | https://bio.tools/nebcutter | SCR_010664 | 2026-08-11 09:42:12 | 151 | ||||||||
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Iran National Tumor Bank Resource Report Resource Website 1+ mentions |
Iran National Tumor Bank (RRID:SCR_010666) | biomaterial supply resource, tissue bank, material resource | Not yet vetted by NIF curator | nlx_73151 | SCR_010666 | 2026-08-11 09:42:07 | 1 | ||||||||||||
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TfSiteScan Resource Report Resource Website 10+ mentions |
TfSiteScan (RRID:SCR_010667) | service resource, analysis service resource, data analysis service, production service resource | The Tfsitescan tool is for promoter sequence analysis and works best with sequences of ~500 nt. Simply enter the nucleic acid sequence in one of the common sequence formats (IG, Genbank, EMBL, GCG, DNAStrider, or Fasta). | has parent organization: IFTI-Mirage | nlx_73876 | SCR_010667 | 2026-08-11 09:42:18 | 43 | |||||||||||
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Asterand Resource Report Resource Website 1+ mentions |
Asterand (RRID:SCR_010703) | Asterand | biomaterial supply resource, tissue bank, material resource | Provides human tissue for drug discovery scientists. * Human Biospecimens: Frozen & Fixed Human Tissues; Human RNA/DNA; Human Primary Cells / Cell lines; Custom Procurement; Oncology tissue, biofluid and RNA sets at special prices * Human Tissue-Based Services: Gene Expression, Molecular Pathology, Biochemical Pharmacology, Metabolism and Toxicity * Predictive Human Disease Models |
is listed by: One Mind Biospecimen Bank Listing is related to: University of Michigan Human Breast Cancer Cell Lines |
nlx_88875 | SCR_010703 | Asterand: Partners in Human Tissue Research, Asterand plc | 2026-08-11 09:42:18 | 6 |
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