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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   

•   Source: SciCrunch Registry

http://gpcr.usc.edu/#nogo

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://tools.thermofisher.com/content/sfs/manuals/Man-XCALI-97194-BioWorks-331-SP1-User-ManXCALI97194-B-EN.pdf

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   

•   Source: SciCrunch Registry

http://www.gromacs.org

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   

•   Source: SciCrunch Registry

http://www.bioclipse.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://autodock.scripps.edu/

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   

•   Source: SciCrunch Registry

http://fsa.sourceforge.net/

Software for a statistical multiple sequence alignment algorithm which uses a "distance-based" approach to align homologous protein, RNA or DNA sequences. The GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned.

Proper citation: FSA (RRID:SCR_016114) Copy   

•   Source: SciCrunch Registry

https://github.com/nvalimak/fsm-lite

Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data.

Proper citation: Fsm-lite (RRID:SCR_016115) Copy   

•   Source: SciCrunch Registry

https://github.com/bbuchfink/diamond

Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search.

Proper citation: DIAMOND (RRID:SCR_016071) Copy   

•   Source: SciCrunch Registry

http://acb.qfab.org/acb/glam2/

Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.

Proper citation: Glam2 (RRID:SCR_016129) Copy   

•   Source: SciCrunch Registry

http://www.functionalnet.org/humannet/about.html

Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes.

Proper citation: HumanNet (RRID:SCR_016146) Copy   

•   Source: SciCrunch Registry

https://www.intomics.com/inbio/map/#home

Database for investigating and visualizing protein-protein interactions. It aims to maintain coverage, quality, convenience, and transparency in the field of PPI research.

Proper citation: inBio Map (RRID:SCR_016147) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/Harmonizome/

Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources.

Proper citation: Harmonizome (RRID:SCR_016176) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/rna-viz-proto

A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.

Proper citation: ToRNADo (RRID:SCR_002706) Copy   

•   Source: SciCrunch Registry

http://www.moleculardevices.com/Products/Software/Meta-Imaging-Series/MetaMorph.html

Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression.

Proper citation: MetaMorph Microscopy Automation and Image Analysis Software (RRID:SCR_002368) Copy   

•   Source: SciCrunch Registry

http://blocks.fhcrc.org/blocks/codehop.html

This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) Copy   

•   Source: SciCrunch Registry

https://www.proteinspire.org/MOPED/

An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.

Proper citation: MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/help/uniprotkb

Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.

Proper citation: UniProtKB (RRID:SCR_004426) Copy   

•   Source: SciCrunch Registry