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

Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2014) Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. Journal of Computer-Aided Molecular Design, 28 3: 221-233. doi:10.1007/s10822-014-9713-7

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Author Koziara, Katarzyna B.
Stroet, Martin
Malde, Alpeshkumar K.
Mark, Alan E.
Title Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies
Journal name Journal of Computer-Aided Molecular Design   Check publisher's open access policy
ISSN 0920-654X
1573-4951
Publication date 2014-01-30
Year available 2014
Sub-type Article (original research)
DOI 10.1007/s10822-014-9713-7
Volume 28
Issue 3
Start page 221
End page 233
Total pages 13
Place of publication Dordrecht, Netherlands
Publisher Springer Netherlands
Language eng
Formatted 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.
Keyword SAMPL4
Automated topology builder
GROMOS
Hydration free enthalpy
Molecular dynamics
Thermodynamic integration
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 30 January 2014

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
 
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Created: Fri, 14 Feb 2014, 20:24:40 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences