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Nicholls A.,OpenEye Scientific Software Inc.
Journal of Computer-Aided Molecular Design | Year: 2012

In asking what progress might occur in molecular modeling in the next 25 years it is worth asking what progress has been made in the last twenty-five. In doing so it is hard to be optimistic for the future of the field unless a greater commitment is made to basic science. © 2011 Springer Science+Business Media B.V. Source


Nicholls A.,OpenEye Scientific Software Inc.
Journal of Computer-Aided Molecular Design | Year: 2012

Molecular modeling and the art of computeraided drug discovery seldom make much use of statistics, despite being fields that can not calculate important properties with great reliability. The 2013 CADD Gordon conference intends to examine what prevents a more effective use of statistics in routine modeling and to raise consciousness as to what is possible. Practical methods will be discussed, deeper issues in applying standard approaches addressed and research on successes and failures in other disciplines presented by invited experts. © Springer Science+Business Media Dordrecht 2012. Source


Nicholls A.,OpenEye Scientific Software Inc.
Journal of Computer-Aided Molecular Design | Year: 2016

The calculation of error bars for quantities of interest in computational chemistry comes in two forms: (1) Determining the confidence of a prediction, for instance of the property of a molecule; (2) Assessing uncertainty in measuring the difference between properties, for instance between performance metrics of two or more computational approaches. While a former paper in this series concentrated on the first of these, this second paper focuses on comparison, i.e. how do we calculate differences in methods in an accurate and statistically valid manner. Described within are classical statistical approaches for comparing widely used metrics such as enrichment, area under the curve and Pearson’s product-moment coefficient, as well as generic measures. These are considered of over single and multiple sets of data and for two or more methods that evince either independent or correlated behavior. General issues concerning significance testing and confidence limits from a Bayesian perspective are discussed, along with size-of-effect aspects of evaluation. © 2016 The Author(s) Source


Nicholls A.,OpenEye Scientific Software Inc.
Journal of Computer-Aided Molecular Design | Year: 2014

Computational chemistry is a largely empirical field that makes predictions with substantial uncertainty. And yet the use of standard statistical methods to quantify this uncertainty is often absent from published reports. This article covers the basics of confidence interval estimation for molecular modeling using classical statistics. Alternate approaches such as non-parametric statistics and bootstrapping are discussed. © The Author(s) 2014. Source


Patent
OpenEye Scientific Software Inc. | Date: 2011-11-14

A method, computing apparatus, and computer readable medium, for augmenting and displaying a 2D-representation of a molecular structure, or assemblage of molecular structures, augmented with various graphical elements. The technology further provides various functionality that permits a user to define the form and number of types of graphical elements to apply to a 2-D structure.

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