OpenEye Scientific Software Inc.

Santa Fe, NM, United States

OpenEye Scientific Software Inc.

Santa Fe, NM, United States
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Patent
OpenEye Scientific Software Inc. | Date: 2015-10-22

The technology encompasses new uses of already-known cryptographic techniques. The technology entails computer-based methods of sharing information securely, in particular an asymmetric method of secure computation that relies on the private-key/public key paradigm with homomorphic encryption. The methods and programmed computing apparatuses herein harness mathematical concepts and apply them to services or tasks that are commercially useful and that have not hitherto been possible. Applications of the methods and apparatus herein are far-ranging and include, but are not limited to: purchase-sale transactions such as real estate or automobiles, where some aspect of price negotiation is expected; stock markets; legal settlements; salary negotiation; auctions, and other types of complex financial transactions.


Patent
OpenEye Scientific Software Inc. | Date: 2016-10-24

The technology encompasses new uses of already-known cryptographic techniques. The technology entails computer-based methods of sharing information securely, in particular an asymmetric method of secure computation that relies on the private-key/public key paradigm with homomorphic encryption. The methods and programmed computing apparatuses herein apply mathematical concepts to services or tasks that are commercially useful and that have not hitherto been possible. Applications of the methods within cloud computing paradigms are presented. Applications of the methods and apparatus herein are far-ranging and include, but are not limited to: purchase-sale transactions such as real estate or automobiles, where some aspect of price negotiation is expected; stock markets; legal settlements; salary negotiation; auctions, and other types of complex financial transactions.


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.


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)


Word J.M.,OpenEye Scientific Software Inc. | Nicholls A.,OpenEye Scientific Software Inc.
Proteins: Structure, Function and Bioinformatics | Year: 2011

The results of two rounds of blind pK a predictions for ionizable residues in staphylococcal nuclease using OpenEye's legacy protein pK a prediction program based on the Zap Poisson-Boltzmann solver were submitted to the 2009 prediction challenge organized by the Protein pK a Cooperative and first round predictions were discussed at the corresponding June 2009 Telluride conference. To better understand these results, 21 additional sets of predictions were performed with the same program, varying the internal dielectric, reference pK a, partial charge set, and dielectric boundary. The internal dielectric (ε{lunate} p) and dielectric boundary were the two most important factors contributing to the quality of the predictions. Although the lowest overall errors were observed with a molecular dielectric boundary at ε{lunate} p = 8, predictions using a smooth Gaussian dielectric boundary performed almost as well at lower ε{lunate} p values because the Gaussian boundary implicitly accounts for a significant level of solvent penetration. Improved pK a predictions with the Gaussian boundary methodology will require better prediction and modeling of structural changes due to changes in ionization state, perhaps without resorting to the more exhaustive sampling of conformational states used by other recent continuum methods. © 2011 Wiley-Liss, Inc.


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.


Trademark
OpenEye Scientific Software Inc. | Date: 2016-01-12

Providing downloadable software for use in analyzing, screening, comparing, constructing, organizing, visualizing, sharing, ordering, annotating, and predicting the behavior and properties of molecules and sets of molecules in the field of science.


Wlodek S.,OpenEye Scientific Software Incorporated | Skillman A.G.,OpenEye Scientific Software Incorporated | Nicholls A.,OpenEye Scientific Software Incorporated
Journal of Chemical Theory and Computation | Year: 2010

A method of rapid entropy estimation for small molecules in vacuum, solution, and inside a protein receptor is proposed. We show that the Hessian matrix of second derivatives built by a quasi-Newton optimizer during geometry optimization of a molecule with a classical molecular potential in these three environments can be used to predict vibrational entropies. We also show that a simple analytical solvation model allows for no less accurate entropy estimation of molecules in solution than a physically rigorous but computationally more expensive model based on Poisson's equation. Our work also suggests that scaled particle theory more precisely estimates the hydrophobic part of solvation entropy than the using a simple surface area term. © 2010 American Chemical Society.


Patent
OpenEye Scientific Software Inc. | Date: 2013-06-17

Methods of securing the calculation of pairwise molecular similarity coefficients between molecules, from similarity measures that are based on 3-dimensional or 2-dimensional molecular properties and/or physicochemical properties, condensed into a fingerprint or bit-string representation, in such a way that a third party cannot deduce information about the underlying molecular structures. The apparatus and process are particularly applicable to generating secured or anonymized databases of bit-strings, so that the anonymized databases can be stored remotely from a corporations computer system, or shared securely and confidentially with another company. The mapping key that permits the anonymized bit strings to be converted back to their original form need not be disclosed outside of the corporation. The methods also permit two companies to exchange molecular structure data securely and in a manner that permits similarity calculations to be performed within as well as between the respective databases.


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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