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https://www.trophoblast.cam.ac.uk/Resources/BioInformatics

Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training.

Proper citation: University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

http://topaz.gatech.edu/GeneMark/

Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.

Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy   

•   Source: SciCrunch Registry

http://geneontology.org/docs/go-consortium/

Consortium integrates resources from variety of research groups, from model organisms to protein databases to biological research communities actively involved in development and implementation of Gene Ontology. Mission to develop up to date, comprehensive, computational model of biological systems, from molecular level to larger pathways, cellular and organism level systems.

Proper citation: GO Gene Ontology Consortium and Knowledgebase (RRID:SCR_017505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://vbspt.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/industrial/spectroscopy-elemental-isotope-analysis/molecular-spectroscopy/fluorometers/qubit/qubit-fluorometer.html

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   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://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