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Commercial antibody vendor which supplies antibodies and other products to life science researchers.
Proper citation: Novus Biologicals (RRID:SCR_004286) Copy
https://www.thermofisher.com/order/catalog/product/Q33238
Qubit fluorometer designed to accurately measure DNA, RNA, and protein quantity, and now also RNA integrity and quality. Qubit 4 Fluorometer was re-engineered to enable data transfer via WiFi as well as to run Qubit RNA IQ assay. Qubit 4 Fluorometer and RNA IQ Assay Kit work together to accurately distinguish intact from degraded RNA in two steps.
Proper citation: Thermo Fisher: Invitrogen: Qubit 4 Fluorometer with WiFi (RRID:SCR_026883) Copy
http://www.sanger.ac.uk/resources/software/vagrent/
Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences.
Proper citation: VAGrENT (RRID:SCR_005180) Copy
http://anya.igsb.anl.gov/Geneways/GeneWays.html
System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.
Proper citation: GeneWays (RRID:SCR_000572) Copy
http://www.cephalopod.org/DBMR.cfm
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Loligo opalescens, L. pealeii, and L. plei can be obtained seasonally on request. The chambered nautilus, Nautilus pompilius, and Octopus bimaculoides are available on request. Animal costs vary by species and size. Any tissue or body fluid from these animals can also be provided. Fees for special services are negotiated on a case-by-case basis.
Proper citation: National Resource Center for Cephalopods (RRID:SCR_002864) Copy
http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
A protein family specific platform that works closely with the GPCR community to determine the high resolution structure and function of GPCRs. Structures are available in the glutamate, secretin, frizzled/TAS2, adhesion, and rhodopsin branches of the protein phylogenetic tree. Users can access a list of protein structure targets and completed protein structures.
Proper citation: GPCR Network (RRID:SCR_014286) Copy
http://www.matrixscience.com/server.html
A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.
Proper citation: Mascot (RRID:SCR_014322) Copy
A a configurable software package for peptide and protein mass spectrometry analyses. It includes the SEQUEST search algorithm to identify separate proteins in complex mixtures, interactive navigation tools to filter and sort protein summaries, customized spectral plots, and chromatograms using the PEPMATCH and PEPMAP tools. This software also has batch processing capabilities to improve throughput by queuing up several files, and custom-build proprietary databases, index databases, and retrieve databases through a public server.
Proper citation: BioWorks (RRID:SCR_014594) Copy
Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FATCAT (RRID:SCR_014631) Copy
Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.
Proper citation: GROMACS (RRID:SCR_014565) Copy
Open source downloadable application which contains a framework for managing and analyzing chemical compounds, as well as supports editing in 2D, processing large collections of molecules in tables, calculate various types of properties, and more cheminformatics functionality. This software also is used for the management and analysis of biological sequences (DNA, RNA, and protein), and relates the chemical structures and a target and then describes them using mathematical descriptors and models them using statistical methods. Bioclipse is equipped with a scripting language (Bioclipse Scripting Language or BSL) which can be used to automate tasks or create reusable snippets that can be shared with others,
Proper citation: Bioclipse (RRID:SCR_014914) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.
Proper citation: Autogrid (RRID:SCR_015982) Copy
http://sing.ei.uvigo.es/ALTER/
Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.
Proper citation: ALTER (RRID:SCR_015968) Copy
Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.
Proper citation: Structural Genomics Consortium (RRID:SCR_003890) Copy
A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database.
Proper citation: WholeCellKB (RRID:SCR_004104) Copy
Consortium to develop efficient and safe strategies for the production of clinical-grade protein pharmaceuticals in plants, and to define the procedures needed for the production of these proteins in compliance with the strict regulatory standards that govern the manufacture of all pharmaceuticals. Ultimately the consortium aimed to take a candidate product all the way through the development pipeline culminating in a phase I human clinical trial. The consortium has a wide range of expertise spanning the areas of molecular biology, plant biology, immunology, recombinant protein expression technology, vaccinology, and plant biotechnology. The objectives listed at the beginning of the Pharma-Planta project are as follows: # To produce a recombinant pharmaceutical molecule in transgenic plants, which will be developed through all regulatory requirements, GMP (good manufacturing practice) standards and pre-clinical toxicity testing. This will then be evaluated in Phase I human clinical trials. # To develop robust risk assessment practices for recombinant pharmaceutical molecules produced in plants, based on health and environmental impact, working with regulatory authorities within the EU as well as public groups to ensure that the production systems are as safe and as acceptable as possible, and that they comply with all biosafety regulations. # To define and carry out a coordinated program for securing and managing intellectual property that will facilitate the availability of high priority plant-derived recombinant pharmaceuticals to the poor in developing countries while simultaneously allowing the products to be developed commercially in Europe and North America. # To develop and refine new strategies for the expression of recombinant pharmaceuticals in plants, which can be used on a generic basis for molecules that are normally expressed poorly. # To develop and generate transgenic plants expressing a second generation of recombinant molecules that will be used in future clinical trials. In 2011 they reached their benchmark for success launching a phase I clinical study of an antibody that neutralizes HIV, produced in and isolated from tobacco plants. This antibody could one day become an inexpensive component of a microbicide used to prevent the spread of HIV/AIDS. The project has also spun off many additional technologies that are being adopted by researchers all over the world, and has resulted in more than 100 publications in peer-reviewed scientific journals.
Proper citation: Pharma-Planta Consortium (RRID:SCR_003880) Copy
The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.
Proper citation: PDBe - Protein Data Bank in Europe (RRID:SCR_004312) Copy
http://www.science.mcmaster.ca/biochem/faculty/truant/truantlab.htm
THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 21, 2013. Laboratory portal of Ray Truant, PhD. It provides an image gallery and videos.
Proper citation: Ray Truant Lab (RRID:SCR_004301) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi
Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.
Proper citation: NCBI BLAST (RRID:SCR_004870) Copy
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