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

Abstract

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.

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Acknowledgments

The development of the ATB has been supported by the Australian Research Council (ARC; Grant No.: DP0987043, ARC DP110100327, ARC DP130102153) AKM acknowledges the award of an Australian Post-Doctoral (APD) fellowship. KBK acknowledges the award of the University of Queensland International Scholarship (UQI). Computational resources were provided by the National Computational Infrastructure (NCI, Australia) National Facility (projects m72 and n63). Support from the Queensland Cyber Infrastructure Foundation and NeCTAR is gratefully acknowledged. The authors also wish to thank W. Chen, M. El-Kebir, G. Klau and D. Warne for assistance in the development of the ATB version 2.0 and associated infrastructure.

Author information

Correspondence to Alan E. Mark.

Additional information

Katarzyna B. Koziara and Martin Stroet have contributed equally to the work.

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Koziara, K.B., Stroet, M., Malde, A.K. et al. Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. J Comput Aided Mol Des 28, 221–233 (2014). https://doi.org/10.1007/s10822-014-9713-7

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Keywords

  • SAMPL4
  • Automated topology builder
  • GROMOS
  • Hydration free enthalpy
  • Molecular dynamics
  • Thermodynamic integration