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http://www.thesgc.org/

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   

•   Source: SciCrunch Registry

http://www.pharma-planta.net/

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   

•   Source: SciCrunch Registry

http://www.wholecellkb.org/

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   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pdbe/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/philius/

Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions.

Proper citation: Philius (RRID:SCR_004625) Copy   

•   Source: SciCrunch Registry

http://www.pantherdb.org/

System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PANTHER (RRID:SCR_004869) Copy   

•   Source: SciCrunch Registry

http://www.proteopedia.org/

Free, collaborative 3D, interactive encyclopedia of proteins and other molecules, it collects, organizes and disseminates structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists. With a free user account, users can edit pages in Proteopedia. Click on the green links to change the 3D image or click and drag the molecules. Categories include Diseases & Related Topics, Enzymes, Gene Expression & Replication, Metabolism, Signaling & Transport, Structural Biology and Miscellaneous. Currently, Proteopedia has 93,912 articles (pages), and 2,366 registered users (May 2013). Among other pages, Proteopedia contains one page (or article) for every entry in the World Wide Protein Data Bank. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are seeded automatically to include a default view of the asymmetric unit, the abstract of the publication, green links to sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random page, you nearly always get one of these automatically-seeded, PDB-code-titled pages (click Random Page in the navigation box at the upper left), because of their abundance. In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure.

Proper citation: Proteopedia - Life in 3D (RRID:SCR_004647) Copy   

•   Source: SciCrunch Registry

http://smart.embl.de/

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Proper citation: SMART (RRID:SCR_005026) Copy   

•   Source: SciCrunch Registry

https://github.com/farshidrayhanuiu/iDTI-ESBoost

Software tool for identification of Drug Target Interaction using Evolutionary and Structural features with Boosting. Used to predict drug-protein interactions.

Proper citation: iDTI-ESBoost (RRID:SCR_016720) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html

Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

Proper citation: Entrez (RRID:SCR_016640) Copy   

•   Source: SciCrunch Registry

https://www.omicsnet.ca/

Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites).

Proper citation: OmicsNet (RRID:SCR_016724) Copy   

•   Source: SciCrunch Registry

http://ec2-52-91-98-53.compute-1.amazonaws.com/run/

Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.

Proper citation: Clonotator (RRID:SCR_016730) Copy   

•   Source: SciCrunch Registry

https://www.proteinmetrics.com/products/byonic/

Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.

Proper citation: PMI-Byonic (RRID:SCR_016735) Copy   

•   Source: SciCrunch Registry

http://metascape.org/gp/index.html#/main/step1

Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.

Proper citation: Metascape (RRID:SCR_016620) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Biostrings.html

Software package for efficient manipulation of biological strings. Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Proper citation: Biostrings (RRID:SCR_016949) Copy   

•   Source: SciCrunch Registry

https://omicssimla.sourceforge.io

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy   

•   Source: SciCrunch Registry

http://prosightlite.northwestern.edu/

Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data.

Proper citation: ProSight Lite (RRID:SCR_016908) Copy   

•   Source: SciCrunch Registry

http://nrtdp.northwestern.edu/

Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.

Proper citation: National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) Copy   

•   Source: SciCrunch Registry