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Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

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• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software used for modeling, simulation, and rendering of 3-D models. The tool is designed to provide a starting point to model, animate, work with lighting, and create VFX.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

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.

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• SciCrunch
• 11 years ago - submitted by Yueling Li

A graphical source code file used for an automated motion detection and reward system for animal training (see comment for full paper title). It was designed on the LabVIEW programming system. Running the program requires the appropriate LabVIEW runtime software from National Instruments Corporation.

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• SciCrunch
• 11 years ago - by Anonymous

A software tool which provides a means to acquire and analyze time-series data, as well as a direct route to publication quality graphics. It provides a variety of graph styles and automated, extended, and/or customizable analyses.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously.

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• SciCrunch
• 11 years ago - submitted by Gabrielle Pine

Software designed to provide an image analysis software solution for offline analysis of images, ideally for the analysis of images where image capture is not required. Available applications for MCID Analysis include gel/blot analysis, fluorescence microscopy, and stereology.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software for browsing the image data acquired by Nikon C1 and a Nikon C1si system.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

A sweep-based data acquisition and analysis software package. Its uses range from a simple storage oscilloscope to complex applications requiring stimulus generation, data capture, control of external equipment and custom analysis. A built-in script language automates tasks and provides additional tools for custom analyses and applications. Signal includes functions for specific application areas, including dynamic clamp, whole cell and patch clamp electrophysiology, and evoked response including control of magnetic and other stimulus devices. Video tutorials and a demo version of Signal is available on the main page.

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• SciCrunch
• 11 years ago - submitted by Jessica Cabotaje

Software which can automatically detect descriptor classes defined in the CDK QSAR descriptor dictionary. Groups of descriptors and individual descriptors can be selected for evaluation. Input can be SDF or SMI formats, while output can be a variety of delimited text formats, annotated SDF or ARFF. The software can also evaluate fingerprints. A summary overview of the available descriptors and their names are available on the website.

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• SciCrunch
• 11 years ago - submitted by Gergo Barta

An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.

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• SciCrunch
• 11 years ago - submitted by Gergo Barta

Software toolkit containing tools to render and canonicalize SMILES and manipulate MOL file and related formats, as well as structure fingerprinting.

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• SciCrunch
• 11 years ago - submitted by Gergo Barta