Combinatorial library software tools | Drug discovery data analysis
Advances in virtual screening have created new channels for expediting the process of discovering novel drugs. Of particular relevance and interest are in silico techniques that enable the enumeration of combinatorial chemical libraries, generation of 3D coordinates and assessment of their propensity for drug-likeness.
Assists users in chemicals combinatorial libraries designing. GLARE is a free software, based on a deterministic greedy procedure, which allows a multi-criterion filtering of reagents according to the researchers’ requests. It aims to give an efficient overview of all reagents that can be combined and to reduce the duration of their examination.
Performs many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. It can predict ligands that can be easily synthesized for subsequent testing in biochemical assays. The tool mimics the azide-alkyne Huisgen cycloaddition, a representative reaction that has been called the ‘‘cream of the crop’’ of click chemistry. It facilitates interactions between computational and synthetic chemists.
Allows users to search and compare chemicals databases. ChemCom matches chemical similarities by using the Tanimoto similarity score and four implemented algorithms. Each query can be stored accompanied by its specific parameters, reused and shared. Besides, the software allows one to run searches from a database indexed by user.
Chooses the minimal subsets from chemical libraries that avoids the necessity of parameterization to the largest extent possible. JEDA allows users to define the size of the library that they wish to create. It is based on a search algorithm and scoring function that take into account information regarding the concentrations of chemical space occupied by a library. This tool aims to minimize the negative effects of the parameterization required by partition-based diversity metrics.
Enumerates and profiles virtual compounds. Library synthesizer is a design and enumeration application that permits to work with Markush structure. Several properties and options are available such as logP, logS, molar refractivity, molecular weight, or H-bond acceptor. Users can also specify the starting material for each R-group and the reagents for each R-group position.
Performs combinatorial library design. CCLab is composed of five modules: (1) Input module parses parameters from the input file, (2) CCLib module assembles the fragments into molecules and builds libraries on line, (3) CCScore module evaluates multiple properties of the libraries, (4) MOGA module executes optimization with the multi-objective genetic algorithm and (5) the main module integrates the modules above, performs the iterations of optimization and collects the output information during the library design process.