Confab - Systematic generation of diverse low-energy conformers

Abstract

BackgroundMany computational chemistry analyses require the generation of conformers, either on-the-fly, or in advance. We present Confab, an open source command-line application for the systematic generation of low-energy conformers according to a diversity criterion.ResultsConfab generates conformations using the 'torsion driving approach' which involves iterating systematically through a set of allowed torsion angles for each rotatable bond. Energy is assessed using the MMFF94 forcefield. Diversity is measured using the heavy-atom root-mean-square deviation (RMSD) relative to conformers already stored. We investigated the recovery of crystal structures for a dataset of 1000 ligands from the Protein Data Bank with fewer than 1 million conformations. Confab can recover 97% of the molecules to within 1.5 Å at a diversity level of 1.5 Å and an energy cutoff of 50 kcal/mol.ConclusionsConfab is available from http://confab.googlecode.com.

Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

“…However, the precision of the S conf highly depends on the accuracy of enumerating the molecular conformers which itself is an active research area. 31,66,67 Comparison of different chemical categories showed that the RMSD and MSE obtained for the predicted standard entropies of compounds containing electron-withdrawing amine-or hydroxyl (secondary alcohols, phenols, and primary amines) moieties as well as compounds with thioether group are higher than other chemicals (Table VI). Similarly, the deviation from experimental enthalpy of formation obtained for nonhydrogens, amino acids, and halogenated compounds is high in comparison to other compound classes (Table III).…”

“…(2) overestimates Ω because rotatable bonds are usually hindered by a potential barrier 30 and not all possible conformations are thermally accessible at room temperature and hence do not contribute to the partition function. 31 Therefore, we approximate ln(Ω) by α to alleviate the overestimation. The empirical approximation for the conformational entropy then becomes…”

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

“…Second, the parameterization and conformational search steps of the algorithm are still being improved, partially based on future user experience with various probe molecules. Currently the server generates conformers for the additional probe molecules using the program Confab 45 . The parameterization involves well established computational chemistry programs including ANTECHAMBER 46 based on the general AMBER force field (GAFF) 47 , and General Atomic and Molecular and Electronic Structure Systems (GAMESS) 48 .…”

Hyperascyrones A–H, polyprenylated spirocyclic acylphloroglucinol derivatives from Hypericum ascyron Linn.

“…Conformational analyses were carried out for compounds 1, 2, 4, and 8 using both BALLOON (Vainio and Johnson, 2007) and confab (O' Boyle et al, 2011) programs. The BALLOON program searches conformational space with genetic algorithm, whereas the confab program systematically generates diverse low energy conformations that are supposed to be close to crystal structures.…”