Nanome, Inc.

University of California

Steven Robert McCloskey

Yang Zhou

Kai Wang

Benjamin Hugh Bratton

Taylor Philip Horwood

Vincent Brunet

Keita William Funakawa

A system and method for molecular design and simulation is disclosed. In one aspect, a system for simulating a molecular structure includes a processor configured to simulate the molecular structure, a head-mounted display (HMD) configured to display the molecular structure, and at least one handheld input device. The input device may be configured to: receive input from a user, the input being indicative of movement of the handheld input device in 6 degrees-of-freedom (DoF), and selectively map, based on additional user input and at least one property of the molecular structure, one of the DoF to one of a plurality of defined techniques for altering the molecular structure. The processor may be configured to modify the molecular structure based on the received input as mapped to the selected defined technique.

Head-mounted display and/or virtual reality video output and mapping handheld input degrees-of-freedom to properties of molecular structure

System that generates the solvent-excluded surface (SES) of a molecule using a parallel algorithm that may execute on a GPU. Parallel execution allows a SES to be created in seconds even for a large protein, or to be recreated rapidly when exploring modifications to molecular structure. The algorithm calculates a spatial field that represents a signed distance between an atom-facing surface of a probe and each point in 3D grid. Spatial field calculations for different grid points may be performed in parallel. The SES is then obtained as the zero isosurface of the spatial field, using for example marching cubes. Atoms and probes may be placed into spatial buckets and indexed by bucket to improve efficiency by limiting calculations to atoms and probes in the proximity of a point.

System that rapidly generates a solvent-excluded surface

Growing community of inventors

San Diego, CA, United States of America

Steven Robert McCloskey