Journal
JOURNAL OF MOLECULAR MODELING
Volume 21, Issue 8, Pages -Publisher
SPRINGER
DOI: 10.1007/s00894-015-2729-7
Keywords
Intermolecular interactions; Nonempirical potentials; Exchange repulsion; Optimal analytical function
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Funding
- Wroclaw Research Centre EIT+ within the project Biotechnologies and advanced medical technologies - BioMed [POIG.01.01.02-02-003/08]
- European Regional Development Fund (Operational Programme Innovative Economy) [1.1.2]
- Polish Ministry of Science and Higher Education
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The repulsion term in conventional force fields constitutes a major source of error. Assuming that this could originate from a too simple analytical functional form, we analyzed various analytical functions using ab initio exchange component values as a reference and obtained (alpha + beta R-1) exp(-gamma R) as the optimal form to represent the repulsion term. Universal exchange, delocalization, and electrostatic penetration potentials approximating the corresponding interaction energy components defined within hybrid variation-perturbation theory (HVPT) were derived using as a reference a training set of 660 biomolecular complexes. The electrostatic multipole term was calculated using cumulative atomic multipole moments, whereas correlation contribution including dispersion term and first-order correlation correction was estimated from non-empirical D-as functions derived by Pernal et al. The resulting non-empirical atom-atom potentials (NEAAP) were tested for several urokinase-inhibitor complexes yielding improved docking results.
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