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http://www.inteligand.com/ligandscout/

Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule.

Proper citation: LigandScout (RRID:SCR_014889) Copy   

•   Source: SciCrunch Registry

https://www.omicron-laser.de/english/lasers/diode-lasers/phoxx-lasers/phoxx-diode-laser.html

Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.

Proper citation: PhoxX Controller (RRID:SCR_016309) Copy   

•   Source: SciCrunch Registry

https://www.axionbiosystems.com/products/axis-software

Software for multi electrode array recording for Axion Biosystems. Used in enhancing cardiac and neural analysis through data processing and signal monitoring.

Proper citation: AxIS (RRID:SCR_016308) Copy   

•   Source: SciCrunch Registry

https://www.charmm.org/charmm/?CFID=66837e22-4ee5-47ba-bcbf-b4b385c2397e&CFTOKEN=0

Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools.

Proper citation: CHARMM (RRID:SCR_014892) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/FINDTHECAT

Software that conducts a jspsych test for response time evaluation. Used in the ABCD Study.

Proper citation: FINDTHECAT (RRID:SCR_016036) Copy   

•   Source: SciCrunch Registry

http://www.getpaint.net/

Software tool as image and photo editor for PCs that run Windows. Features user interface with support for layers, unlimited undo, special effects, and variety of useful and powerful tools.

Proper citation: paint.net (RRID:SCR_017641) Copy   

•   Source: SciCrunch Registry

http://gaussian.com/

Software program for electronic structure modeling that enables researchers to study and predict the properties of molecules and reactions under a wide range of conditions, especially those that are difficult or impossible to observe experimentally.

Proper citation: Gaussian (RRID:SCR_014897) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/Jaguar

Ab initio molecular modeling software program that computes an array of molecular properties such as multipole moments, polarizabilities, and electrostatic potential. It can also map reaction coordinates between reactants, products, and transition states.

Proper citation: Jaguar (RRID:SCR_014895) Copy   

•   Source: SciCrunch Registry

https://github.com/ebtrexler/NetSuite

Software for dynamic clamping. It uses National Instruments Boards.

Proper citation: NetClamp (RRID:SCR_016275) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/stroop-task

Software that conducts the Stroop Color Task. Used in the ABCD Study.

Proper citation: stroop-task (RRID:SCR_016033) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/MIES

Software for Electrophysiology functions. It was developed by the Allen Institute.

Proper citation: MIES (RRID:SCR_016443) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/ReadCleaner4Scaffolding

This pipeline and the included scripts are used to filter useful reads for SSPACE.

Proper citation: ReadCleaner4Scaffolding (RRID:SCR_016166) Copy   

•   Source: SciCrunch Registry

https://musescore.org/en

Music composition and manipulation software.

Proper citation: MuseScore (RRID:SCR_016161) Copy   

•   Source: SciCrunch Registry

https://github.com/ekg/fastahack

Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.

Proper citation: Fastahack (RRID:SCR_016090) Copy   

•   Source: SciCrunch Registry

http://www.wavefun.com/

Software program for determining molecular structure and calculating chemical properties. It has a graphical interface and accurate computational models that are compatible with the iPad, iPhone and iPod Touch. When combined with the Spartan'16 Parallel Suite, this enables the first fully-functional open-ended molecular modeling environment on popular mobile technology.

Proper citation: SPARTAN (RRID:SCR_014901) Copy   

•   Source: SciCrunch Registry

http://www.fujitsu.com/jp/group/kyushu/en/solutions/industry/lifescience/admeworks/

Software program for high-speed virtual screening intended for simultaneous evaluation of ADMET properties of compounds. ADMEWORKS Predictor employs a number of models to predict ADMET properties using models based on values of topological, geometric, physicochemical and substructure descriptors derived from the molecular structures.

Proper citation: ADMEWORKS Predictor (RRID:SCR_014905) Copy   

•   Source: SciCrunch Registry

http://www.optibrium.com/stardrop/index.php

Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.

Proper citation: StarDrop (RRID:SCR_014902) Copy   

•   Source: SciCrunch Registry

http://brainbox.pasteur.fr/

Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.

Proper citation: BrainBox (RRID:SCR_014750) Copy   

•   Source: SciCrunch Registry

http://autopatcher.org/

Software tool for neuronal recording in intact brain.

Proper citation: Autopatcher (RRID:SCR_017464) Copy   

•   Source: SciCrunch Registry

https://compumedicsneuroscan.com/product/stim2-precise-stimulus-presentation/

Soft­ware envi­ron­ment for custom stim­u­lus and task design as well as presen­ta­tion. Compumedics Neuroscan’s design system which can be inte­grated in fMRI, MEG, and other func­tional neuro-imaging appli­ca­tions. Provides inter­face to design and present visual and audi­tory stim­u­la­tion paradigms.

Proper citation: Stim2 (RRID:SCR_016751) Copy   

•   Source: SciCrunch Registry