New additions and updates
McQSAR: A Multiconformational Quantitative Structure−Activity Relationship Engine Driven by Genetic Algorithms
McQSAR, an extension to the traditional GA approach to derive QSARs. McQSAR is able to use descriptors for multiple representations per compound, such as different conformers, tautomers, or protonation forms. Test runs show that the algorithm converges to a set of representations that describe the binding mode of the set of input molecules to a reasonable resolution provided that suitable descriptors based on the three-dimensional structure are used.
Mikko J. Vainio and Mark S. Johnson (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J. Chem. Inf. Model. 45, 1953-1961 DOI.
The recently updated Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and confomer ensembles using a multi-objective genetic algorithm. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.