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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
http://dichroweb.cryst.bbk.ac.uk/html/home.shtml
Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures.
Proper citation: DichroWeb (RRID:SCR_018125) Copy
https://web.expasy.org/protparam/
Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
Proper citation: ProtParam Tool (RRID:SCR_018087) Copy
https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/
Collection of SARS-CoV-2 sequences currently available in GenBank genetic sequence database and Sequence Read Archive. Updated as additional sequences are released.
Proper citation: SARS-CoV-2-Sequences (RRID:SCR_018319) Copy
http://huanglab.phys.hust.edu.cn/hpepdock/
Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations.
Proper citation: HPEPDOCK Server (RRID:SCR_018561) Copy
http://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE
Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation.
Proper citation: GalaxyRefine (RRID:SCR_018531) Copy
http://crdd.osdd.net/raghava/toxinpred/
Software package for peptides designing and prediction. In silico approach for predicting toxicity of peptides and proteins. Used for predicting peptide toxicity or non toxicity, minimum mutations in peptides for increasing or decreasing their toxicity, toxic regions in proteins.
Proper citation: ToxinPred (RRID:SCR_018542) Copy
https://sciex.com/products/software/proteinpilot-software
Software tool for protein identification and relative protein expression analysis. Used in protein research to identify proteins and search large numbers of post translational modifications. Compatible with all proteomics MS/MS systems.
Proper citation: ProteinPilot Software (RRID:SCR_018681) Copy
Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models.
Proper citation: BcForms (RRID:SCR_018654) Copy
https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
Web tool for detection of structural and functional domains in protein sequences. Allows computation and download of conserved domain annotation for large sets of protein queries. Allows to view results graphically. Shows domain footprints, alignment details, and conserved features on any individual query sequence.
Proper citation: Batch Web CD-Search Tool (RRID:SCR_018756) Copy
https://www.iitm.ac.in/bioinfo/PPA_Pred/index.html
Web server for protein protein affinity prediction. Used for predicting binding affinity of protein protein complexes.
Proper citation: PPA-Pred2 (RRID:SCR_018957) Copy
Web based database of proteins, RNA, lipids and metabolites that are identified in extracellular vesicles. Compendium for extracellular vesicles with continuous community annotation and with manually curated data from published literature.
Proper citation: Vesiclepedia (RRID:SCR_019011) Copy
http://www.softberry.com/berry.phtml?topic=fgenes_plus&group=programs&subgroup=gfs
Web tool as HMM plus similar protein based gene prediction. Used for multiple gene prediction in genomic DNA with using information from similar protein. Used if you know protein sequence similar with protein which is encoded by gene in your sequence.
Proper citation: FGENESH Plus (RRID:SCR_018937) Copy
http://msquant.sourceforge.net/
Software tool for quantitative proteomics,mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.Entry in MSQuant is Mascot search engine.
Proper citation: MSQuant (RRID:SCR_019206) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.
Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy
http://www.jstacs.de/index.php/GeMoMa
Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species.
Proper citation: GeMoMa (RRID:SCR_017646) Copy
https://github.com/soedinglab/hh-suite
Software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Used for sequence-based protein function and structure prediction what depends on sequence-search sensitivity and accuracy of the resulting sequence alignments.
Proper citation: HH-suite (RRID:SCR_016133) Copy
https://www.schrodinger.com/protein-preparation-wizard
Software tool for correcting common structural problems and creating reliable, all atom protein models.
Proper citation: Protein preparation Wizard (RRID:SCR_016749) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
http://www.cbs.dtu.dk/services/NetPhos/
Web tool as artificial neural network method that predicts phosphorylation sites in independent sequences. Web application based on determination of activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. NetPhos 3.1 server predicts serine, threonine or tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. Generic predictions are identical to predictions performed by NetPhos 2.0. Kinase specific predictions are identical to predictions by NetPhosK 1.0. NetPhos 3.1 is available as stand-alone software package.
Proper citation: NetPhos (RRID:SCR_017975) Copy
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