Bioinformatics workflow tools | Drug discovery data analysis
There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package.
An open source chemistry toolbox. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Provides tools for cheminformatics, computational chemistry, and predictive modeling. RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. RDKit provides tools for 2D and 3D molecular operations, descriptor and fingerprint generation for machine learning, molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators, cheminformatics nodes for KNIME.
Facilitates the implementation of software packages in chemoinformatics. The CDK is an open-source Java library uses as the basis for other open-source projects. Besides its proven usability in research and production quality scientific software, the CDK has also become a valuable tool for teaching chemoinformatics. The functionality is provided for many areas in cheminformatics including molecule and reaction valence bond representation, canonical identifiers for fast exact searching and many others.
Allows intuitive hierarchical structuring, visualization and analysis of complex structure and bioactivity data. Scaffold Hunter reads data, for example, from biochemical screens, extracts chemically meaningful compound scaffolds (that is, all carbo- and heterocyclic rings, their aliphatic linker bonds and atoms attached via a double bond) and iteratively removes one ring at a time from the larger child scaffolds to generate smaller ‘parent’ scaffolds according to a set of chemistry- and medicinal chemistry–derived rules. Scaffold Hunter has its origin in drug discovery, which is still one of the main application areas, and is evolved into a reusable open source platform for a wider range of applications.
Assists users with computer-aided drug design. CADDSuite provides several tools for data storage and retrieval, data preparation, chemical checks, quantitative structure-activity relationship (QSAR), docking, rescoring and for the analysis of results. Tools of this suite share a common binary interface, a common data exchange format and are integrate into distributed computing environments.
Aims to fulfill the need for comprehensive and open source drug discovery software. ODDT was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. It reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible.
Provides a set of command line programs for cheminformatics and structure-based design. Chemalot contains more than 30 sub tools. It can be used to perform basic and complex cheminformatics tasks that range from (1) merging of structural and numerical data, (2) selecting diverse sets of compounds from a library and, (3) creating machine learning models to performing 3D analyses such as the computation of ligand strain and quantum mechanical torsion scans.