Abstract: Computer-based methods that permit two or more users to perform simultaneous edits on a digitally encoded molecular structure. The methods use properties of conflict-free replicated data types (CRDT's) and causal trees to provide a distributed system which can manage the life-cycle of virtual molecular structures; including simultaneous editing, versioning, and provenance. Applications of the technology include, but are not limited to: simultaneous computer aided design of molecules in 2D or 3D in which users may be distributed across multiple computers and in which the need for computer time synchronization (offline or online editing) is obviated; version control and provenance tracking of a virtual molecule; and other types of data used in computer aided molecular design activities.

Abstract: 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.

Abstract: 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.

Abstract: 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 corporation's 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.

Abstract: 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.

Abstract: I describe several methods for organizing databases of molecular structures and searching such structures. Also described are methods for characterizing molecules based on the shapes of their fields that can be used in conjunction with the methods of organizing and searching databases. In particular, the databases of molecular structures can be analyzed by a shape metric technique, and the parameters of the decomposition can be used in creating, characterizing, and searching databases of molecules based on field similarity. The most immediate application of these techniques is to pharmaceutical drug discovery and design.

Abstract: I describe several techniques for characterizing molecules based on the shapes of their fields. In particular, I describe a way to automatically break molecules into a series of fragments by using an ellipsoidal Gaussian decomposition. These fragments can then be analyzed by a shape metric technique, and the parameters of the decomposition can be used in creating, characterizing, and searching databases of molecules based on field similarity. The ellipsoidal Gaussian representations can also be used to describe binding or active sites on macromolecules, thereby providing a template for searching for complementary molecules in a database. The most immediate application of these techniques is to pharmaceutical drug discovery and design.

Abstract: I describe several techniques for characterizing molecules based on the shapes of their fields. In particular, I describe a way to automatically break molecules into a series of fragments by using an ellipsoidal Gaussian decomposition. These fragments can then be analyzed by a shape metric technique, and the parameters of the decomposition can be used in creating, characterizing, and searching databases of molecules based on field similarity. The ellipsoidal Gaussian representations can also be used to describe binding or active sites on macromolecules, thereby providing a template for searching for complementary molecules in a database. The most immediate application of these techniques is to pharmaceutical drug discovery and design.

Abstract: I describe several methods for organizing databases of molecular structures and searching such structures. Also described are methods for characterizing molecules based on the shapes of their fields that can be used in conjunction with the methods of organizing and searching databases. In particular, the databases of molecular structures can be analyzed by a shape metric technique, and the parameters of the decomposition can be used in creating, characterizing, and searching databases of molecules based on field similarity. The most immediate application of these techniques is to pharmaceutical drug discovery and design.