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http://www.ingenuity.com/

A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base .

Proper citation: Ingenuity Pathways Knowledge Base (RRID:SCR_008117) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/ipd/mhc/bola/

This website is intended to be the definitive source of information on the bovine major histocompatibility complex - its genes, proteins and polymorphism. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The BoLA nomenclature committee is a standing committee of the International Society for Animal Genetics. Its purpose is to collate data on the Bovine Leucocyte Antigens (BoLA) and provide a forum for the analysis and nomenclature of polymorphisms in the genes and proteins of the bovine MHC. The information gathered here is based on the BoLA workshop reports, which are published in Animal Genetics and the European Journal of Immunogenetics. The workshop report data are reproduced with the permission of the publishers Blackwell Science, and other text on the site is used with the permission of CRC Press.

Proper citation: BoLA Nomenclature: International Society for Animal Genetics (RRID:SCR_008142) Copy   

•   Source: SciCrunch Registry

http://topdb.enzim.hu

Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.

Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/asd/altsplice/index.html

AltSplice is a computer generated high quality data set of human transcript-confirmed splice patterns, alternative splice events, and the associated annotations. This data is being integrated with other data that is generated by other members of the ASD consortium. The ASD project will provide the following in its three year duration: -human curated database of alternative spliced genes and their properties -a computer generated database of alternatively spliced genes and their properties -the integration of the above and newly found knowledge in a user-friendly interface and research workbench for both bioinformaticists and biologists -DNA chips that are based on the data in the above databases -the DNA chips will be used to test against predisposition for and diagnoses of human diseases ASD aims to analyse this mechanism on a genome-wide scale by creating a database that contains all alternatively spliced exons from human, and other model species. Disease causing mutations seem to induce aberrations in the process of splicing and its regulation. The ASD consortium will develop a DNA microarray (chip) that contains cDNAs of all the splicing regulatory proteins and their isoforms, as well as a chip that contains a number of disease relevant genes. We will concentrate on three models of disease (breast cancer, FTDP-17, male infertility) in which a connection between mis-splicing and a pathological state has been observed. Finally, these chips will be developed as demonstrative kits to detect predisposition for and diagnosis of such diseases. Categories: Nucleotide Sequences: Gene Structure, Introns and Exons, & Splice Sites Databases

Proper citation: AltSplice Database of Alternative Spliced Events (RRID:SCR_008162) Copy   

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http://dimer.tamu.edu/doodle/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view.

Proper citation: Database of oligomerization domains from lambda experiments (RRID:SCR_008107) Copy   

•   Source: SciCrunch Registry

http://jbirc.jbic.or.jp/hinv/ppi/

The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program.

Proper citation: H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/peptide-synthesis/

Core facility that provides services such as peptide synthesis, incorporation of non-conventional and/or modified amino acids, HPCL characterization and purification, and Mass spec analysis.

Proper citation: Salk Institute Peptide Synthesis Core Facility (RRID:SCR_014848) Copy   

•   Source: SciCrunch Registry

https://aideepmed.com/COACH/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.molsoft.com/icm_browser.html

Molecular graphics environment which provides biologists and chemists with representations of proteins, DNA, RNA, and multiple sequence alignments. Users can build, annotate, and edit interactive views and slides of molecules. Users can also superimpose protein structures, search PDB, measure distanaces and angles, and view and make high resolution images of alignments.

Proper citation: ICM Browser (RRID:SCR_014878) Copy   

•   Source: SciCrunch Registry

http://medblast.sibsnet.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs.

Proper citation: MedBlast (RRID:SCR_008202) Copy   

•   Source: SciCrunch Registry

http://www.poissonboltzmann.org/apbs/

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods.

Proper citation: Adaptive Poisson-Boltzmann Solver (RRID:SCR_008387) Copy   

•   Source: SciCrunch Registry

http://www.jcsg.org/

The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898).

Proper citation: Joint Center for Structural Genomics (RRID:SCR_008251) Copy   

•   Source: SciCrunch Registry

http://portal.ncibi.org/gateway/gin.html

GIN-IE is a high precision system for extracting protein/gene interactions, interaction cue words, and directionality from the literature. Syntax-aware inferences about the roles of the entities are made by using the syntactic and dependency parse tree structures of the sentences. Negation and speculation are frequently occurring language phenomena that modify the factuality of the information contained in text. GIN-IE detects and distinguishes interactions that are extracted from negated or speculative sentences. GIN-IE has been integrated with the NCIBI PubMed daily update and processing pipeline. The extracted interactions are accessible through MimiWeb.

Proper citation: Gene Interaction Extraction from the Literature (RRID:SCR_008660) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.ingenuity.com/products/pathways_analysis.html

A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest.

Proper citation: Ingenuity Pathway Analysis (RRID:SCR_008653) Copy   

•   Source: SciCrunch Registry

https://www.bio-rad.com/en-us/product/bio-plex-200-systems?ID=715b85f1-6a4e-41b3-b5d9-80202d779e13

Suspension array system which offers protein and nucleic acid researchers multiplex assay solution permiting analysis of up to 100 biomolecules in single sample.

Proper citation: Bio-Rad: Bio-Plex 200 System (RRID:SCR_018026) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/IMGTrepertoire/

Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system.

Proper citation: IMGT Repertoire (RRID:SCR_018220) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fluorometers/qubit/qubit-fluorometer.html

Benchtop fluorometer designed to accurately measure DNA, RNA, and protein quantity. Measures RNA integrity and quality. Touch screen to select and run assays with results displayed in few seconds.

Proper citation: Thermo Fisher: Qubit fluorimeter (RRID:SCR_018095) Copy   

•   Source: SciCrunch Registry

http://homes.gersteinlab.org/Khurana-PLoSCompBio-2013/

Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network.

Proper citation: MultiNet (RRID:SCR_016149) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nsegata/phylophlan/wiki/Home

Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloPhlAn (RRID:SCR_013082) Copy   

•   Source: SciCrunch Registry