Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies

• Published in: Journal of computer-aided molecular design Vol. 28; no. 3; pp. 221 - 233
• Main Authors: Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K., Mark, Alan E.
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.03.2014; Springer Nature B.V
• Subjects: Algorithms; Animal Anatomy; Automated; Chemical compounds; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Computer Simulation; Construction; Dissolution; Dynamical systems; Dynamics; Enthalpy; Errors; Histology; Hydration; Models, Chemical; Molecular structure; Morphology; Pharmaceutical Preparations - chemistry; Physical Chemistry; Solvents; Thermodynamics; Topology; Water - chemistry; Molecular dynamics; Automated topology builder; SAMPL4; Thermodynamic integration; Hydration free enthalpy; GROMOS
• ISSN: 0920-654X; 1573-4951; 1573-4951
• DOI: 10.1007/s10822-014-9713-7

To test and validate the Automated force field Topology Builder and Repository (ATB; http://compbio.biosci.uq.edu.au/atb/ ) the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment. The calculations were performed using a fully automated protocol that incorporated a dynamic analysis of the convergence and integration error in the selection of intermediate points. The system has been designed and implemented such that hydration free enthalpies can be obtained without manual intervention following the submission of a molecule to the ATB. The overall average unsigned error (AUE) using ATB 2.0 topologies for the complete set of 214 molecules was 6.7 kJ/mol and for molecules within the SAMPL4 7.5 kJ/mol. The root mean square error (RMSE) was 9.5 and 10.0 kJ/mol respectively. However, for molecules containing functional groups that form part of the main GROMOS force field the AUE was 3.4 kJ/mol and the RMSE was 4.0 kJ/mol. This suggests it will be possible to further refine the parameters provided by the ATB based on hydration free enthalpies.