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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://mordred.bioc.cam.ac.uk/~rapper/rampage.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure.
Proper citation: RAMPAGE (RRID:SCR_017590) Copy
Software package for analysis of single particle diffusion trajectories, where diffusion constants switch randomly according to Markov process. Analytical tool to combine information from thousands of short single-molecule trajectories of intracellularly diffusing proteins. Has ability to learn number of diffusive states directly from data, in addition to model parameters such as transition rates and diffusion constants.
Proper citation: vbSPT (RRID:SCR_017554) Copy
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
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
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
http://proteom.ibb.waw.pl/mscan/
Software tool for analysis of qualitative data, operating on basis of lists of peptides and proteins identified in samples generated by Mascot database system. Responsible for preparing data for quantitative analysis of proteins both with use of stable isotope labeling and without isotope labeling.
Proper citation: MascotScan (RRID:SCR_018201) Copy
http://prodata.swmed.edu/promals3d/promals3d.php
Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.
Proper citation: PROMALS3D (RRID:SCR_018161) Copy
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
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
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