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Elking D.M.,OpenEye Scientific Software
Journal of Computational Chemistry | Year: 2016

New equations for torque and atomic force are derived for use in flexible molecule force fields with atomic multipoles. The expressions are based on Cartesian tensors with arbitrary multipole rank. The standard method for rotating Cartesian tensor multipoles and calculating torque is to first represent the tensor with n indexes and 3n redundant components. In this work, new expressions for directly rotating the unique (n + 1)(n + 2)/2 Cartesian tensor multipole components Θpqr are given by introducing Cartesian tensor rotation matrix elements X(R). A polynomial expression and a recursion relation for X(R) are derived. For comparison, the analogous rotation matrix for spherical tensor multipoles are the Wigner functions D(R). The expressions for X(R) are used to derive simple equations for torque and atomic force. The torque and atomic force equations are applied to the geometry optimization of small molecule crystal unit cells. In addition, a discussion of computational efficiency as a function of increasing multipole rank is given for Cartesian tensors. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Geballe M.T.,OpenEye Scientific Software | Guthrie J.P.,University of Western Ontario
Journal of Computer-Aided Molecular Design | Year: 2012

Prediction of the free energy of solvation of a small molecule, or its transfer energy, is a necessary step along the path towards calculating the interactions between molecules that occur in an aqueous environment. A set of these transfer energies were gathered from the literature for series of chlorinated molecules with varying numbers of chlorines based on ethane, biphenyl, and dibenzo-p-dioxin. This focused set of molecules were then provided as a blinded challenge to assess the ability of current computational solvation methods to accurately model the interactions between water and increasingly chlorinated compounds. This was presented as part of the SAMPL3 challenge, which represented the fourth iterative blind prediction challenge involving transfer energies. The results of this exercise demonstrate that the field in general has difficulty predicting the transfer energies of more highly chlorinated compounds, and that methods seem to be erring in the same direction. © Springer Science+Business Media B.V. 2012.

McGann M.,OpenEye Scientific Software
Journal of Computer-Aided Molecular Design | Year: 2012

The docking performance of the FRED and HYBRID programs are evaluated on two standardized datasets from the Docking and Scoring Symposium of the ACS Spring 2011 national meeting. The evaluation includes cognate docking and virtual screening performance. FRED docks 70 % of the structures to within 2 A in the cognate docking test. In the virtual screening test, FRED is found to have a mean AUC of 0.75. The HYBRID program uses a modified version of FRED's algorithm that uses both ligand- and structure-based information to dock molecules, which increases its mean AUC to 0.78. HYBRID can also implicitly account for protein flexibility by making use of multiple crystal structures. Using multiple crystal structures improves HYBRID's performance (mean AUC 0.80) with a negligible increase in docking time (̃15 %). © Springer Science+Business Media B.V. 2012.

Cannon E.O.,OpenEye Scientific Software
Journal of Chemical Information and Modeling | Year: 2012

We propose a new, robust benchmark, called Percentage Round Tripping of Canonical Isomeric SMILES (%RTCS), for assessing the ability of chemical nomenclature software to convert chemical structures to names and chemical names to structures. The benchmark is based on a string comparison between canonical isomeric SMILES generated from the original structure and the resultant structure from round tripping. Using the latest version of the OpenEye chemical nomenclature toolkit, Lexichem v2.1.0, we report %RTCS values of over 92% on average for a variety of challenging compound collections. © 2012 American Chemical Society.

Nicholls A.,OpenEye Scientific Software
Methods in molecular biology (Clifton, N.J.) | Year: 2011

An understanding of simple statistical techniques is invaluable in science and in life. Despite this, and despite the sophistication of many concerning the methods and algorithms of molecular modeling, statistical analysis is usually rare and often uncompelling. I present here some basic approaches that have proved useful in my own work, along with examples drawn from the field. In particular, the statistics of evaluations of virtual screening are carefully considered.

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