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Showing 14 open source projects for "qsar"
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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ReinventCommunity
Jupyter Notebook tutorials for REINVENT 3.2
This repository is a collection of useful jupyter notebooks, code snippets and example JSON files illustrating the use of Reinvent 3.2. -
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JRC QSAR Model Database
(Q)SAR Model Reporting Format Inventory
In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf... -
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QSAR Dataset Division GUI
Dataset division GUI is a user friendly QSAR dataset division tool
The purpose of this application tool is to perform rational selection of training and test set using Kennard Stone algorithm, diversity based and activity based division method. -
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QSAR Data Pretreatment
To remove the constant and highly correlated descriptors based on user
Before performing the actual chemometric analysis in QSAR, the raw data is usually pretreated due to following reasons: 1. To remove those descriptor whose values remains more or less constant for all compounds, since they only add computing time without contributing much to the results. 2. To reduce collinearity among the descriptors thereby preventing data over-fitting and aids in improving the prediction performance of the model. -
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QSAR Kennard Stone
Kennard Stone algorithm based division
The purpose of this program is to perform rational selection of training and test set based on Kennard Stone algorithm: -
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QSAR Qualitative Validation
Qualitative validation of QSAR models
The purpose of this program is to verify the ability of the QSAR/Pharmacophore model to distinguish significantly between the two classes (i.e. active and inactive molecules). It is based on calculation of different qualitative validation parameters such as sensitivity, specificity, precision, accuracy, and F-measure. -
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MLR Y randomization
This test is performed to check the robustness of the QSAR model
This test is performed to check the robustness of the QSAR model by building several random models via shuffling the dependent variables, while keeping the independent variables as it is. The resultant random models are expected to have significantly low r^2 and q^2 values for several trials, to pass the test. Another parameter, cRp^2 is also calculated, which should be more then 0.5 for passing this test. -
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QSAR is a project that aims to build a GUI that enables people to build quantitative structure activity (or property) relationship models. It will use parts of CDK (cdk.sf.net), JOELib (joelib.sf.net), R (www.r-project.org) and other projects.
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Train and Validate QSAR models using state-of-the-art learning algorithms like SVM. Build classification and regression and use them to make predictions. The whole project is intended to serve the need for toxicological predictions.
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SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
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mySQL db app that stores chemical structures, calc. descriptors and property values. It has a descriptor calculator and a method that filters descriptors correlated with property values. Easy to plug-in your descriptor calc. Ideal for QSAR specialists!
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ddutils (drug design utils) contains programs and libraries applied in drug design. It is designed to cover all fields in CADD, such as ADME, QSAR, MD, molecular docking, solvation effect and free energy prediction.
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The JAQPOT3 web services are OpenTox API-1.2 compliant web services. JAQPOT3 is a web application that supports model training and data preprocessing algorithms such as MLR, SVM, ANN and more.
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