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https://vbrn.org/proteomics-services/
Provides central resource of mass spectrometry based proteomics technologies to identify, characterize and quantify target proteins in various biological and biomedical samples. Provides mass spectrometry expertise for analyzing proteins and peptides for proteomics studies, support for data analysis from proteomics measurements, training in proteomics methods, and experimental design.
Proper citation: Vermont University Proteomics Core Facility (RRID:SCR_018667) Copy
Core provides physicochemical characterization of nanoscale entities. Offers characterization of several classes of nanomaterials:Polymer conjugates,Polymeric micelles,Liposomes,Nanogels,Polyion complexes of small drugs and biomacromolecules (proteins, DNA, and RNA),Inorganic/metal nanoparticles,Bio-derived nanoparticles such as exosomes with protein and nucleic acid cargo.
Proper citation: North Carolina University at Chapel Hill Nanomedicines Characterization Core Facility (RRID:SCR_017951) Copy
Core provides analytical redox biochemistry methods and mentoring support for COBRE junior faculty with goal to advance their research endeavors, publications and fundability. Specific aims are:Provide ROS /RNS identification and quantification, Perform quantitative analysis of ROS/RNS. Provides expertise and technology for in depth biochemical analysis of thiol-centered enzyme activities and define protein:protein interactions.
Proper citation: South Carolina Medical University Analytical Redox Biology Core Facility (RRID:SCR_017955) Copy
http://compbio.cs.princeton.edu/concavity/
Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.
Proper citation: Concavity (RRID:SCR_016063) Copy
http://compbio.cs.princeton.edu/conservation/
Software for scoring protein sequence conservation using the Jensen-Shannon divergence. It can be used to predict catalytic sites and residues near bound ligands.
Proper citation: Conservation (RRID:SCR_016064) Copy
Biomedical technology research center that develops new technology for NMR spectroscopy and makes it available to the biomedical research community for structure determination of proteins in biological supramolecular assemblies, such as membrane proteins or virus particles. The principal applications are to membrane-associated proteins; however, the approach is generally applicable to polypeptides that cannot be prepared in forms suitable for X-ray crystallography or multidimensional solution NMR spectroscopy. As a result, there are also applications to viruses and other biological systems. The principal instrumentation consists of high-field NMR spectrometers dedicated to high-resolution solid-state NMR spectroscopy. The spectrometers are capable of the full-range of multiple-resonance experiments on stationary and spinning samples; however, the major emphasis is on methods that utilize mechanically or magnetically oriented samples. Development encompasses preparation of samples, including: * Expression and purification of membrane proteins * Design and construction of instrumentation, especially probes * Implementation of new pulse sequences and other experimental protocols for solid-state NMR spectroscopy * Calculations for the processing of experimental data and protein structure determination from the orientational constraints derived from these data
Proper citation: UCSD Center for NMR Spectroscopy and Imaging of Proteins (RRID:SCR_001401) 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.glycosciences.de/glycocd/
Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.
Proper citation: Glyco-CD (RRID:SCR_001574) Copy
https://www.tamuk.edu/agriculture/institutes-and-other-units/nntrc/Products-Services.html
Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville.
Proper citation: National Natural Toxins Research Center (RRID:SCR_002824) Copy
http://www.uniprot.org/program/Chordata
Data set of manually annotated chordata-specific proteins as well as those that are widely conserved. The program keeps existing human entries up-to-date and broadens the manual annotation to other vertebrate species, especially model organisms, including great apes, cow, mouse, rat, chicken, zebrafish, as well as Xenopus laevis and Xenopus tropicalis. A draft of the complete human proteome is available in UniProtKB/Swiss-Prot and one of the current priorities of the Chordata protein annotation program is to improve the quality of human sequences provided. To this aim, they are updating sequences which show discrepancies with those predicted from the genome sequence. Dubious isoforms, sequences based on experimental artifacts and protein products derived from erroneous gene model predictions are also revisited. This work is in part done in collaboration with the Hinxton Sequence Forum (HSF), which allows active exchange between UniProt, HAVANA, Ensembl and HGNC groups, as well as with RefSeq database. UniProt is a member of the Consensus CDS project and thye are in the process of reviewing their records to support convergence towards a standard set of protein annotation. They also continuously update human entries with functional annotation, including novel structural, post-translational modification, interaction and enzymatic activity data. In order to identify candidates for re-annotation, they use, among others, information extraction tools such as the STRING database. In addition, they regularly add new sequence variants and maintain disease information. Indeed, this annotation program includes the Variation Annotation Program, the goal of which is to annotate all known human genetic diseases and disease-linked protein variants, as well as neutral polymorphisms.
Proper citation: UniProt Chordata protein annotation program (RRID:SCR_007071) Copy
http://sbcb.bioch.ox.ac.uk/cgdb/
A database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations.
Proper citation: CGDB (RRID:SCR_011959) Copy
https://www.moffitt.org/research-science/shared-resources/proteomics-and-metabolomics/
Provides instrumentation for proteomics and metabolomics studies, including protein, peptide and metabolite separations, MS instrumentation for protein, peptide and metabolite analysis, and data systems, software, and bioinformatics tools for data archiving and analysis. Proteomics Core performs routine analytical proteomics services, including target discovery, identification and quantitation, and also provides platforms for functional proteomics using variety of strategies for protein separation, sub-proteome enrichment, post-translational modification analysis, and quantitation.
Proper citation: Moffitt Cancer Center Proteomics and Metabolomics Core Facility (RRID:SCR_012168) Copy
https://github.com/Wssduer/GraphRBF
Software tool as protein-protein/nucleic acid interaction site prediction model built by enhanced graph neural networks and prioritized radial basis function neural networks. Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.
Proper citation: GraphRBF (RRID:SCR_025652) Copy
https://github.com/KarchinLab/HotMAPS
Software tool to detect somatic mutation hotspot regions in 3D protein structures.
Proper citation: HotMaps (RRID:SCR_027725) Copy
Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources.
Proper citation: PathoMAN (RRID:SCR_026552) Copy
https://www.tgh.org/institutes-and-services/cancer-institute/precision-medicine-bio-repository
Procures high-quality biologic specimens along with coded clinical and demographic data across broad ethnic, racial, and social demographic of patients. All specimens are systematically collected and processed so that their multi-functional potential for recovering high-quality bioanalytes (including RNA, genomic DNA, protein, enzymes and metabolites) is conserved. All specimens are stored and protected in a database hub to connect researchers conducting variety of scientific projects across multiple medical specialties. Muilti-disciplinary biorepository with capacity for generating specialized bioanalytes.
Proper citation: Tampa General Hospital-University of South Florida Health Precision Medicine Biorepository (RRID:SCR_027501) Copy
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