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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Relibase Resource Report Resource Website 1+ mentions |
Relibase (RRID:SCR_014888) | data or information resource, database, software resource, web application | Web-based system for searching and analysing protein-ligand structures in the Protein Data Bank (PDB). The database provides an easily accessible web-browser interface and clear 3D structure visualisation that allows for 3D protein-ligand interaction searches, automatic superimposition and detailed analysis of related binding sites to identify protein flexibility, ligand overlap, and conserved water positions. | structural biology, protein, ligand, protein data bank, pdb, visualization, analysis, molecular recognition | Available to the academic community | SCR_014888 | SciCrunch Registry | 2026-10-17 01:28:56 | 5 | |||||||||||
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BatchTINT Resource Report Resource Website 1+ mentions |
BatchTINT (RRID:SCR_014804) | BatchTINTV2, BatchTINTV3 | data analysis software, data processing software, software application, software repository, software resource | GUI created by the Taub Institute in order to create an end-user friendly batch processing solution to complement Axona's new command line modification of TINT. This GUI allows the user to define a directory. Within this directory it will be continuously (unless closed) searching for new files to analyze via TINT. | python, gui, batch processing, tint, axona, directory | Alzheimer’s Association 2015NIRG341570; NIA R01 AG050425 |
DOI:10.5281/zenodo.200977 | Open access, Available for download, Operates on Windows | https://doi.org/10.5281/zenodo.200977 | https://github.com/GeoffBarrett/BatchTINTV2/tree/2.0.0 | SCR_014804 | SciCrunch Registry | BatchTINTV2, BatchTINTV3 | 2026-10-17 01:29:06 | 3 | |||||
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GVKBIO databases Resource Report Resource Website 1+ mentions |
GVKBIO databases (RRID:SCR_014893) | data or information resource, database, software resource, web application | Collection of databases with standalone databases, which gives opportunity for customers to integrate the data into their internal tools and databases, as well as online databases, that are available to the customers from a dedicated website where an individual can query and export the data in the selected format. The standalone database topics include medicinal chemistry, drugs and target class based compounds. The online databases are comprised of three major compilations: GVK BIO Online Structure Activity Relation Database (GOSTAR), GVK BIO Biomarker Database (GOBIOM), and Clinical Trial Outcome Database (CTOD). | research, database, online, standalone, medicinal chemistry, drug, clinical, toxicity, biomarker, contract research organization, cro | Commercial | SCR_014893 | SciCrunch Registry | GVK Biosciences, GVK BIO | 2026-10-17 01:28:50 | 3 | ||||||||||
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iResearch Library Resource Report Resource Website 1+ mentions |
iResearch Library (RRID:SCR_014890) | data or information resource, database, software resource, web application | Database of commercially accessible screening compounds from international chemistry suppliers. iResearchLibrary is updated on a weeky basis and offers support for creating internal screening libraries containing commercially accessible compounds, developing exploratory and targeted libraries, selecting commercially accessible compounds for SAR, lead expansion, and hit follow-up projects, and using structures for pharmacophore searching, virtual screening and other computational work. | research, database, library, chemistry, suppliers, pharmacology, screening, computation | Commercial, Freely available to National Institutes of Health (NIH) researchers | SCR_014890 | SciCrunch Registry | 2026-10-17 01:28:50 | 2 | |||||||||||
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PCSIM Resource Report Resource Website 1+ mentions |
PCSIM (RRID:SCR_014770) | simulation software, software application, software resource | Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI. | simulation software, simulator, heterogenous network, model, neuron, synapse | is related to: CSIM | DOI:10.3389/neuro.11.011.2009 | Available for download | SCR_014770 | SciCrunch Registry | Parallel neural Circuit SIMulator, Parallel Neural Circuit Simulator (PCSIM), Parallel Neural Circuit Simulator | 2026-10-17 01:28:56 | 4 | ||||||||
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World Drug Index Resource Report Resource Website |
World Drug Index (RRID:SCR_014891) | data or information resource, database, software resource, web application | Database of marketed and developed drugs indexed with internationally-recognized drug names, synonyms, trade names, trivial names and trial preparation codes in one source, plus compound structures and activity data. Each record has chemical structure and is classified by drug activity, mechanism of action, treatment, manufacturer, synonyms, medical nformation and literature references. | drug, index, chemical, trade name, generic name, company name, synonyms, compounds, treatment, manufacturer | Commercial | SCR_014891 | SciCrunch Registry | 2026-10-17 01:29:07 | 0 | |||||||||||
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EcoCyte Bioscience Resource Report Resource Website 1+ mentions |
EcoCyte Bioscience (RRID:SCR_014773) | commercial organization | Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology. | supplier, commercial, xenopus, xenopus laevis, laboratory equipment, oocyte, pharmacology, heterologous expression, electrophysiology | is parent organization of: Ecocyte Bioscience Xenopus laevis oocytes delivery service | SCR_014773 | SciCrunch Registry | 2026-10-17 01:28:48 | 6 | |||||||||||
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Genezilla Resource Report Resource Website 10+ mentions |
Genezilla (RRID:SCR_014657) | data analysis software, data processing software, sequence analysis software, software application, software resource | Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites. | eukaryotic gene finder, markov, framework, c++, signal peptide, branch point, tata, cap site | Available for download | SCR_014657 | SciCrunch Registry | 2026-10-17 01:28:54 | 19 | |||||||||||
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Eelbrain Resource Report Resource Website 10+ mentions |
Eelbrain (RRID:SCR_014661) | data analysis software, data processing software, software application, software resource | Statistical analysis toolbox for MEG and EEG. There are three primary data-objects: Factor for categorical variables, Var for scalar variables, and NDVar for multidimensional data. Factor is a container for one-dimensional, categorial data – each case is described by a string label. Var is a container to associate one-dimensional numpy.ndarray objects with a name. NDVars offer numpy functionality that takes into account the dimensions. There is also a Dataset class which acts as a vessel for variable objects (Factor, Var and NDVar) describing the same cases. | statistical analysis, analysis toolbox, electrical brain activity, meg, eeg | is hosted by: GitHub | NYU Abu Dhabi Institute G1001 | Open source, Acknowledgement requested | https://github.com/christianbrodbeck/Eelbrain | SCR_014661 | SciCrunch Registry | 2026-10-17 01:28:48 | 14 | ||||||||
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Zero Mode Waveguide Imaging and Analysis package tools Resource Report Resource Website 1+ mentions |
Zero Mode Waveguide Imaging and Analysis package tools (RRID:SCR_014660) | data acquisition software, data processing software, image analysis software, software application, software resource | MATLAB software tool collection for data acquisition and image analysis from zero mode waveguides. | software tool collection, matlab, data acquisition, image analysis, zero mode waveguide, package tools | is hosted by: GitHub | Available for download, Documentation is currently lacking | https://github.com/marcel-goldschen-ohm | SCR_014660 | SciCrunch Registry | 2026-10-17 01:29:05 | 5 | |||||||||
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MetaboLights Resource Report Resource Website 500+ mentions |
MetaboLights (RRID:SCR_014663) | data or information resource, data repository, database, service resource, storage service resource | A cross-species, cross-technique database for metabolomics experiments, data, and derived information. It includes metabolite structures and their reference spectra, their biological roles, locations and concentrations, and experimental data from metabolic experiments. | metabolomics, database, structure, spectra, experimental data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Metabolomics Workbench |
BBSRC BB/L024152/1 | Publicly available, The community can contribute to this resource | r3d100011556 | SCR_014663 | SciCrunch Registry | MetaboLights | 2026-10-17 01:28:55 | 889 | |||||||
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ToxAlert Resource Report Resource Website 1+ mentions |
ToxAlert (RRID:SCR_014907) | software resource | Software tool for high-throughput toxicity prediction; it assists in the early and quick identification of toxic drug candidates. ToxAlert provides probability percentages for different toxicity endpoints such as oncogenicity, mutagenicity, teratogenicity, neurotoxicity or cell toxicity. | toxicity prediction, modeling, oncogenicity, mutagenicity, teratogenicity, neurotoxicity, cell toxicity | Commercial | SCR_014907 | SciCrunch Registry | 2026-10-17 01:28:50 | 2 | |||||||||||
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Schrodinger Resource Report Resource Website 500+ mentions |
Schrodinger (RRID:SCR_014879) | commercial organization | Commercial ogranization which provides molecular and drug discovery software and services to researchers. American software company that develops chemical simulation software for use in pharmaceutical, biotechnology, and materials science research. Provides products ranging from general molecular modeling programs to a full suite of chemical simulation and drug design software, including ligand- and structure-based methods. | software solution, drug discovery, small molecule, computational chemistry |
is parent organization of: Epik is parent organization of: Ligprep is parent organization of: Glide is parent organization of: Phase is parent organization of: MacroModel is parent organization of: Maestro is parent organization of: Protein preparation Wizard is parent organization of: Shape screening |
Wikidata: Q7432923, ISNI: 0000 0001 0903 5603, grid.421925.9, SCR_014879 | https://ror.org/05a3z6914 | SCR_014879 | SciCrunch Registry | Schrodinger Inc. | 2026-10-17 01:28:49 | 840 | ||||||||
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NeuroExperimenter Resource Report Resource Website 1+ mentions |
NeuroExperimenter (RRID:SCR_014759) | NEx | data analysis software, data processing software, data visualization software, software application, software resource | Software which provides an interface for MindWave Mobile hardware, allowing users to view and listen to brainwave output of different "mind states". Users can: view any or all brainwaves, specify a combination of brainwaves via a formula, compare a base line session to a performance session, and create a log and run it through the application to view different graphical outputs. NeuroExperimenter only runs on Windows | data visualization, data analysis, software, interface, brainwave, brain wave, mind state | Freely available, Available for download, Under active development | https://sites.google.com/site/fredm/neuroexperimenter | SCR_014759 | SciCrunch Registry | NeuroExperimenter (NEx) | 2026-10-17 01:28:56 | 1 | ||||||||
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Mvaspike Resource Report Resource Website |
Mvaspike (RRID:SCR_014760) | simulation software, software application, software resource | Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats. | simulation software, neural network, biological neural network, spiking neural network, event based modeling, event based simulation | SCR_014760 | SciCrunch Registry | 2026-10-17 01:28:48 | 0 | ||||||||||||
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FRED - Fast exhaustive docking Resource Report Resource Website 1+ mentions |
FRED - Fast exhaustive docking (RRID:SCR_014885) | FRED | software resource | Complementary OEDocking tool for virtual screening, it performs a systematic and non-stochastic examination of all possible protein-ligand poses. The software also filters for shape complementarity and chemical feature alignment before selecting and optimizing protein-ligand poses. | docking, protein ligand, protein-ligand, protein ligand interaction, protein-ligand interaction, protein ligand pose, protein-ligand pose, ultra high throughput, compliment | http://docs.eyesopen.com/oedocking/fred.html | SCR_014885 | SciCrunch Registry | Fast exhaustive docking (FRED), Fast exhaustive docking | 2026-10-17 01:29:07 | 1 | |||||||||
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Open National Cancer Institute Database Resource Report Resource Website 10+ mentions |
Open National Cancer Institute Database (RRID:SCR_014886) | data or information resource, database, software resource, web application | Public web server that provides structures, data, tools, programs and other useful information to the public for computer-aided drug design. It is the official database of the Computer-Aided Drug Design (CADD) Group. | drug design, drug testing, computer-aided, web, database, server, computer-aided drug design, cadd | Public, Available to the research communtiy | SCR_014886 | SciCrunch Registry | 2026-10-17 01:28:50 | 10 | |||||||||||
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IonChannelLab Resource Report Resource Website 1+ mentions |
IonChannelLab (RRID:SCR_014762) | simulation software, software application, software resource | Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista. | simulation software, kinetic modeling, ion channel, electrophysiology | CONACyT Mexico 79897; CONACyT Mexico 105457; NINDS R01 NS032337 |
Available for download | SCR_014762 | SciCrunch Registry | 2026-10-17 01:29:06 | 5 | ||||||||||
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libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | simulation software, software application, software resource | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | SciCrunch Registry | 2026-10-17 01:28:49 | 11 | ||||||
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La Jolla Institute for Immunology Resource Report Resource Website 1+ mentions |
La Jolla Institute for Immunology (RRID:SCR_014845) | institution | Institute dedicated to research in immunology by utilizing the academic and research communities in the La Jolla area as well as technological advances in biomedical research, imaging and analysis. Specific topics include autoimmune disease, cancer, allergies, infectious diseases and inflammation. | la jolla, allergy, immunology, biomedical, research, autoimmune disease, cancer, allergy, infectious disease, inflammation |
is parent organization of: La Jolla Institute for Immunology Clinical Studies Core Facility is parent organization of: La Jolla Institute for Immunology Bioinformatics Core Facility is parent organization of: La Jolla Institute for Immunology Microscopy and Histology Core Facility is parent organization of: La Jolla Institute for Immunology Flow Cytometry Core Facility |
, Wikidata Q6463245, ISNI 0000 0004 0461 3162, GRID grid.185006.a | https://ror.org/05vkpd318 | SCR_014845 | SciCrunch Registry | 2026-10-17 01:28:56 | 3 |
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