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Database of hundreds of thousands of products submitted by reagent provider partners, and millions of webpages selected from reagent suppliers. All are organized according to genes, species, and reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones, biochemicals, and others).
Proper citation: Labome (RRID:SCR_007384) Copy
http://noble.gs.washington.edu/proj/sdp-svm/
A statistical framework for genomic data fusion is a computational framework for integrating and drawing inferences from a collection of genome-wide measurements. Each dataset is represented via a kernel function, which defines generalized similarity relationships between pairs of entities, such as genes or proteins. The kernel representation is both flexible and efficient, and can be applied to many different types of data. Furthermore, kernel functions derived from different types of data can be combined in a straightforward fashion. Recent advances in the theory of kernel methods have provided efficient algorithms to perform such combinations in a way that minimizes a statistical loss function. These methods exploit semidefinite programming techniques to reduce the problem of finding optimizing kernel combinations to a convex optimization problem. Computational experiments performed using yeast genome-wide datasets, including amino acid sequences, hydropathy profiles, gene expression data and known protein-protein interactions, demonstrate the utility of this approach. A statistical learning algorithm trained from all of these data to recognize particular classes of proteins--membrane proteins and ribosomal proteins--performs significantly better than the same algorithm trained on any single type of data. Matlab code to center a kernel matrix and Matlab code for normalization are available.
Proper citation: A statistical framework for genomic data fusion (RRID:SCR_007219) Copy
http://www.ncbi.nlm.nih.gov/guide/sitemap/
The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation.
Proper citation: NCBI Resource List (RRID:SCR_005628) Copy
http://wiki.c2b2.columbia.edu/califanolab/index.php/BCellInteractome.htm
A network of protein-protein, protein-DNA and modulatory interactions in human B cells. The network contains known interactions (reported in public databases) and predicted interactions by a Bayesian evidence integration framework which integrates a variety of generic and context specific experimental clues about protein-protein and protein-DNA interactions with inferences from different reverse engineering algorithms, such as GeneWays and ARACNE. Modulatory interactions are predicted by the MINDY, an algorithm for the prediction of modulators of transcriptional interactions (please refer to the publication section for more information). The BCI can be downloaded as one tab delimited file containing the complete network (BCI.txt) with each type of interaction explicitly defined.
Proper citation: B Cell Interactome (RRID:SCR_008655) Copy
https://github.com/TransDecoder/TransDecoder
Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.
Proper citation: TransDecoder (RRID:SCR_017647) Copy
http://lincsportal.ccs.miami.edu/dcic-portal/
Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies.
Proper citation: LINCS Data Portal (RRID:SCR_014939) Copy
https://www.synapse.org/#!Synapse:syn4921369/wiki/235539
Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain.
Proper citation: PsychENCODE Knowledge Portal (RRID:SCR_017500) Copy
Web application for protein-ligand binding site prediction. Starting from given structure of target proteins, COACH will generate complementray ligand binding site predictions using two comparative methods, TM-SITE and S-SITE, which recognize ligand-binding templates from the BioLiP protein function database by binding-specific substructure and sequence profile comparisons.
Proper citation: COACH (RRID:SCR_027684) Copy
https://www.ou.edu/structuralbiology/cobre-core-facilities/ppc
Offers access to instrumentation, training, and services for protein expression, purification, and biophysical characterization. In addition to instrument access, PPCC personnel offer advice, hands-on training, education, and collaboration. Provides a range of protein purification and characterization equipment.
Proper citation: University of Oklahoma Protein Production and Characterization Core Facility (RRID:SCR_028067) Copy
Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc.
Proper citation: Amorfix (RRID:SCR_003783) Copy
Commercial company delivering content for personalized medicine in the areas of Biomarker Services, Biomarker Assays, Isobaric and Isotopic Reagents and Proprietary Biomarkers. A global leader in applied proteomics, they use high sensitivity proprietary technologies to detect biomarkers (differentially expressed proteins in diseases) and to develop rapid assays for testing. The biomarkers discovered in body fluids or tissues are validated, developed and commercialized as diagnostic, prognostic or therapeutic products through strategic alliances and out-licensing.
Proper citation: Proteome Sciences (RRID:SCR_004106) Copy
http://www.thebindingsite.com/
Company provides specialist diagnostic products to clinicians and laboratory professionals worldwide. Specialist protein company committed to research, development, manufacture and distribution of immunodiagnostic assays for global laboratory market. Specialized in antibody specificity technology, Binding Site gives clinicians and laboratory staff tools to significantly improve diagnosis and management of those patients with specific cancers and immune disorders. Binding Site manufactures wide range of products for plasma protein analysis including Freelite, Hevylite and SPAplus.
Proper citation: Binding Site (RRID:SCR_004051) Copy
A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.
Proper citation: TANGO (RRID:SCR_001770) Copy
http://thomsonreuters.com/metadrug/
A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization
Proper citation: MetaDrug (RRID:SCR_000461) Copy
Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering.
Proper citation: Abazyme (RRID:SCR_001139) Copy
An antibody supply company that provides reagents targeting all human proteins. Atlas Antibodies develops reagents and antibodies for mass-spectrometry-based quantitative proteomics as well. Their production and development is based on the Human Protein Atlas (HPA) project, which released a complete tissue-based map of human protein expression using antibodies.
Proper citation: Atlas Antibodies (RRID:SCR_001137) Copy
http://sourceforge.net/projects/orfer/
An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.
Proper citation: ORFprimer (RRID:SCR_003269) Copy
A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein.
Proper citation: Rockland Immunochemicals (RRID:SCR_003278) Copy
http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.
Proper citation: SODOCK (RRID:SCR_000193) Copy
http://sourceforge.net/projects/as-peak/
A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.
Proper citation: AS-Peak (RRID:SCR_000380) Copy
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