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https://www.rdocumentation.org/packages/qtl2/versions/0.24
Software R package for mapping quantitative trait loci with high dimensional data and multiparent populations. Used for analysis of high dimensional data and complex crosses. Interactive software environment for mapping quantitative trait loci in experimental populations.R/qtl2 software expands scope of R/qtl software package to include multiparent populations derived from more than two founder strains, such as Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations.
Proper citation: R/qtl2 (RRID:SCR_018181) Copy
Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results.
Proper citation: ClusPro (RRID:SCR_018248) Copy
Software platform to integrate transcription factor gene interactions and validate regulatory networks. Gene regulatory network validation.
Proper citation: ConnecTF (RRID:SCR_022577) Copy
https://github.com/compbiolabucf/APA-Scan
Software Python tool for detection and visualization of annotated and potential alternative polyadenylation events in downstream 3'-UTR of gene among two different biological conditions. Used for detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data.
Proper citation: APA-Scan (RRID:SCR_022974) Copy
http://www.proteometools.org/index.php?id=home
Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.
Proper citation: ProteomeTools (RRID:SCR_018535) Copy
Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.
Proper citation: GlyGen (RRID:SCR_023438) Copy
https://mibig.secondarymetabolites.org/
MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters.
Proper citation: Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) Copy
Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .
Proper citation: BindingDB (RRID:SCR_000390) Copy
https://midasnetwork.us/covid-19/
Portal for COVID-19 modeling research. Public access data collections with documented metadata.Computational models to study transmission dynamics of broad range of infectious diseases.
Proper citation: Modeling Infectious Disease Agents Study online portal for COVID-19 (RRID:SCR_018281) Copy
Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs.
Proper citation: Evolutionary Couplings Server (RRID:SCR_018745) 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
http://web.cbio.uct.ac.za/~darren/rdp.html
Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes.
Proper citation: Recombination Detection Program (RRID:SCR_018537) Copy
Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition.
Proper citation: Datanator (RRID:SCR_018651) Copy
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Proper citation: RiboTaper (RRID:SCR_018880) Copy
Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.
Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy
Software tool for identification of cross-linked peptides from mass spectra. Used for analysis of chemically cross-linked protein complexes. Used to analyze both novel and existing data sets.
Proper citation: Kojak (RRID:SCR_021028) Copy
https://github.com/hms-dbmi/spp
R analysis and processing package for Illumina platform Chip-Seq data.
Proper citation: SPP (RRID:SCR_001790) Copy
A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.
Proper citation: BioCyc (RRID:SCR_002298) Copy
Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.
Proper citation: Community Structure-Activity Resource (RRID:SCR_002206) Copy
A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.
Proper citation: Simtk.org (RRID:SCR_002680) Copy
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