June 2004 - Cool people doing cool projects, Sunyata Molecular Corporation

They use trueSpace to help in creating their compound blueprints, which let them design molecules for everything from medical to agricultural use, and more.

Lisa: Computational modeling of biopharmaceutical molecules has the potential to revolutionize drug discovery. Currently, however, the utility of molecular modeling in drug development is limited due to issues of computational complexity.

Using methods where the computational complexity is low, such as in the case of molecular mechanics calculations, the accuracy and resolution of results is also low. In contrast, ab initio quantum chemistry methods can yield greatly increased accuracy and resolution; however, the computational complexity of these calculations is the rate limiting factor here, even for supercomputers.

New algorithms developed by Sunyata Molecular employ principles of subatomic particle physics to yield more accurate and predictive structures than has been possible using other methods, while at the same time greatly reducing the time and computational power required to produce the results.

Sunyata's in silico reactor technology has the potential to finally bring molecular modeling into the mainstream of drug design and development, speeding up the drug development process and reducing costs in time and manpower.

Tom: Tell us a little about your company, with a brief history? What does it do that is different from other companies?

Lisa: For the most part, a methodology company uses in silico (computer based) or experimental (laboratory based) methods to discover novel molecules. Sunyata Molecular is an in silico molecular analysis and design methodology company that performs subatomic analysis and precision molecule design for top tier industry partners in the biotechnology, pharmaceutical and agrochemical industries.

Sunyata is clearly differentiated because its design process is subatomic. All current methods are grounded in valence theory or the more sophisticated molecular orbital theory, which is the established explanation of how electrons are distributed in stable molecules. In contrast, Sunyata's subatomic science is based on the level of theory of the standard model of fundamental particles and interactions.

These subatomic molecular representations are of extremely high resolution, and are housed in what Sunyata calls “compound blueprints”, which explain in detail the subatomic pathways that give rise to molecular structure and function at an unprecedented level of resolution. Compound blueprints are transactional 3-D multimedia interactive PDF documents with secure remote access to the in silico reactor grid, other blueprints and compatible network interface protocols. The compound blueprint enables continued analysis, morphing, and enhancement to the molecular protostructures, and subatomic analysis within the blueprint.

Lisa: Sunyata's high resolution subatomic analysis requires a novel representation, which Sunyata has addressed by adapting high end modeling and animation technology to implement the Sunyata compound blueprint, which is the output of our design process. Compound blueprints detail the subatomic pathways that give rise to molecular structure and function at a level of resolution that is not possible with current molecular modeling.

Caligari's trueSpace is used as an integral component of Sunyata's compound blueprint authoring and document rendering process pipeline, and greatly facilitates compound blueprint production.

Tom: You are currently developing a plug-in for trueSpace that will help - what will it do?

Lisa: The proprietary plug-in we are developing closely integrates trueSpace with the in silico reactor inputs and outputs in real-time. The in silico reactor is Sunyata's highly automated distributed computational grid that implements our novel subatomic analysis process. Molecules of any size or complexity when inserted into the reactor interact within a containing field and in so doing reveal their unique subatomic pathways. The results are then returned to the authenticated user, via the interactive compound blueprint pdf file.

Tom: What uses are the molecules put to?

Lisa: Applications of the molecules currently range from therapeutic i.e. oncology and other chronic degenerative diseases, to agrochemical crop protection. Also large biomolecules such as proteins or complexes thereof are analyzed to illuminate their dynamics, structure, and function. Ultimately there is no limit to the uses of the molecules we analyze and design. We can analyze and design molecules of all kinds.

Lisa: Coming from a different application domain, Caligari's trueSpace was substantially easier for us to learn, use and apply, and for our application more relevant than competing products we also evaluated. The intuitive interface was a very significant factor.

Tom: What do you like most about your work? What achievements are you most proud of?

Lisa: We believe ultimately that Sunyata science fundamentally redefines and unifies chemistry under a single rubric, i.e. subatomic pathways. Subatomic pathways uniquely describe molecular structure, function, and interactions. In this way molecules large or small are accurately analyzed and formerly designed without the focus on the use of standard computational molecular modeling or other current trial and error methods.

Lisa Wood is the chief executive officer of Sunyata Molecular Corporation. She is a seasoned entrepreneur who spearheaded the company's formation, negotiated and managed Sunyata's science and technology validation contracts, company operations, investor relations, built the advisory board, and developed the company business plan.

During the R&D phase, she managed employees with diverse scientific and engineering backgrounds. She has a proven track record in sales, marketing, team building, and contract negotiation.

Ms. Wood is a former Time Inc., Fortune Magazine publishing industry executive responsible for Sunyata Molecular's initial R&D funding.