Table 1 Examples of chemoinformatic tools available to enumerate virtual chemical libraries
From: Chemoinformatics-based enumeration of chemical libraries: a tutorial
Tool | Main features | References |
|---|---|---|
Free tools | ||
RDKit | Library enumeration is based on generic reactions and that for every one of its generic reactants a list of real reactant structures is provided | [23] |
DataWarrior | Enumerated product structures are generated from a given generic reaction and that for every one of its generic reactants a list of real reactant structures is provided | [19] |
KNIME | Library enumeration is based on generic reactions, where a list of reagent structures is provided for each of its generic reagents | [24] |
Library synthesizer | Enumerated chemical libraries from specifications of central scaffolds with connection points and lists of R groups | [16] |
D-Peptide Builder | A chemoinformatic tool to enumerate combinatorial libraries of up to pentapeptides, linear or cyclic, using the natural pool of 20 amino acids. The user can use non‐ and/or N‐methylated amino acids. The server also enables the rapid visualization of the chemical space of the newly enumerated peptides in comparison with other libraries relevant to drug discovery and preloaded in the server | [21] |
SmiLib v2.0 | Tool for rapid combinatorial library enumeration in the flexible and portable SMILES notation. Combinatorial building blocks are attached to scaffolds by means of linkers, this allows for the creation of customized libraries using linkers of different sizes and chemical nature | [25] |
GLARE (Global Library Assessment of REagents) | Allows to optimize reagent lists for the design of combinatorial libraries | [26] |
Comercial tools | ||
Reactor (ChemAxon) | Library enumeration is based on generic reactions combined with reaction rules; therefore, it is capable of generating chemically feasible products without preselection of reagents | [18] |
Molecular Operating Environment (MOE) | Scaffold Replacement: New chemical compounds are generated by replacing a portion of a known compound (the scaffold), while preserving the remaining chemical groups QuaSAR_CombiGen: A single combinatorial product is constructed by attaching R-groups to a scaffold at marked attachment points, called ports. The entire combinatorial library is enumerated by exhaustively cycling through all combinations of R-groups at every attachment point on every scaffold | [14] |
Schrödinger | Core hopping: Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds | [15] |
Nova (Optibrium) | Enumerated chemical libraries from specifications of central scaffolds with connection points and lists of R groups | [17] |