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MolSoft's New Technology Brings Online Publications to Life in Fully Interactive 3D.

MolSoft LLC Press Release: San Diego, CA. 20th October 2009

Scientific publishing is now going 3D. For the first time in online publishing history, the PLoS ONE journal is publishing original research papers containing fully annotated and interactive 3D objects. This 3D environment provides a "movie-like" experience but with a significant difference - the reader is in control of the scenes and each view is linked directly to the text. This is possible because of a new technology called ActiveICM developed by MolSoft LLC. ActiveICM is now being used for scientific publishing due to a collaboration with scientists at the SGC. Initially the technology is being applied to the life sciences for the 3D display of the atomic structures of molecules implicated in disease. ActiveICM can also be used for any online publication where a 3D view would enhance the subject matter. Click here to see the PLoS ONE collection of papers.

MolSoft LLC has developed this breakthrough, technology (US Patent No:7,880,738) that embeds live 3D objects into online media publications. This new software allows the reader to visualize and explore 3D representations of any object. It is a guide, which brings you from view-to-view and location-to-location, but allows you to explore independently any region of the 3D object. The reader is in control of what he or she wants to view and, with a click of the mouse, the online story comes to life. ActiveICM is popularly referred to as "iSee" - a phrase often expressed by the reader when difficult concepts or new products become easier to appreciate in 3D and coined by scientists at the SGC for use in the collaboration.

Scientists involved in drug discovery have been the first to utilize ActiveICM. Pharmaceutical companies and academic research laboratories around the world are using this technology for their drug and structural data communication. Now you can see this technology applied for the first time in the PLoS ONE, one of the most respected peer-reviewed medical research journals.

PLoS ONE and scientists at SGC have published a new set of scientific papers using ActiveICM. The collection of papers is called "Structural Biology and Human Health: Medically Relevant Proteins from the SGC." This collection of papers enables medical researchers for the first time to view and interact with drug-target molecules in three dimensions while reading a scientific paper. The initial release of papers to PLoS ONE by SGC includes significant medical breakthroughs in the understanding of the structure of molecules involved in cancer cell proliferation and survival, molecules associated with acute motor dysfunction, and atomic details on how the body degrades foreign compounds and poisons.

The PLoS ONE collection of papers contains text hyperlinked directly to the 3D environment. The 3D environment "lends itself" to the reader and the reader can then delve into the object and investigate any region of interest that he or she chooses. Simple navigation through the 3D story is aided by 3D annotation and high quality molecule representations and rendering. For example, the binding properties of the active site region of a protein can be displayed, and a scientist can interpret this 3D representation to design a new drug molecule.

Viewing 3D characteristics of molecules such as DNA and Proteins in 3D is important to understanding how complex molecules in the human body interact and helps scientists develop drugs to target them. Traditionally scientists viewed these molecules in small flat and non-interactive images on their computer screens. They then had to download the 3D coordinates from an external site, display the structure in another piece of software, and then render and annotate the structure, all of which made for a very complicated process. If an author uses ActiveICM, then the reader has all of these steps completed for them and is free to explore the story in 3D immediately in a high quality visualizer embedded into the document.

Professor Ruben Abagyan, MolSoft's Founder and Faculty member at the University of California San Diego said, "This new technology enriches a scientific publication and allows the author of the paper to explain his or her results in a more visual and interactive way. The method developed at MolSoft will transform the way scientists communicate and exchange their data. ActiveICM gives the reader a sense of context, which is missing in all other animated media such as online movies. This truly is a step forward for scientific publishing, and we expect that other branches of science and other industries to take the technology on board."

The software has uses outside of medical research because it can display, render and annotate any kind of 3D object such as a car or a house. MolSoft is excited to be leading the way in this new publication medium and hopes other publishing houses will soon adopt this new technology. The technical details of ActiveICM are described in this month's edition of PLoS ONE in a paper by Eugene Raush (MolSoft), Max Totrov (MolSoft), Brian Marsden (SGC) and Ruben Abagyan (University of California San Diego).

ActiveICM is a free download from MolSoft's website http://www.molsoft.com/activeicm.html .

About MolSoft LLC

Molsoft is a San Diego, California-based company that is a primary source of new breakthrough technologies in molecular graphics, visualization, molecular modeling, docking, virtual screening and cheminformatics. Molsoft offers complete solutions customized for a biotechnology or pharmaceutical company in the areas of computational biology and chemistry.

Laboratories in pharmaceutical and academic laboratories use MolSoft's main software platform called ICM-Pro to solve challenging problems in biology, chemistry and physics. The ICM protein-protein docking software has performed very well in the prediction of how molecules in the cell interact with one another and has won worldwide competitions against our competitors. The software is widely used for the discovery of new lead compounds for drug discovery. ICM-Pro recently delivered a star performance in a challenging competition to predict the interaction of a ligand to a G-Protein Coupled Receptor (GPCR) a key family of drug targets. Recent success stories have included identification of new lead compounds for GPCRs, nuclear receptors, kinases, proteases, and transferases, all of which are involved in a variety of diseases such as cancer, heart disease and obesity.

MolSoft is also dedicated to finding ways to solve problems associated with receptor flexibility upon ligand binding. When a drug molecule binds to the disease causing protein (receptor), there is usually some change in the shape of the protein. Molsoft has developed methods that allow the ligand to mold the conformation of the receptor or by using multiple receptor conformations of the receptor during the compound-screening process.

ActiveICM developed so that scientists can communicate their discoveries to their colleagues in a clear and user-friendly way and has now progressed to a complete tool for scientific publications.

Molsoft is committed to continuous innovation, scientific excellence, the development of cutting-edge technologies and original ideas.

About the SGC

The SGC (www.thesgc.org) is a public-private partnership that was formed to place three dimensional structures of proteins of medical relevance into the public domain, without restriction on use. Its overarching aim is to provide tools and reagents to enable biomedical research and drug discovery. The SGC currently operates out of three laboratories at the Universities of Oxford and Toronto, and at Karolinska Institutet, Stockholm. The research programs derive from a funder-created Target List of ~2,000 proteins, vetted by leading academic and industrial scientists. Targets include human proteins associated with diseases such as cancer, diabetes, inflammation, and genetic disease, as well as proteins from human parasites such as those that cause malaria.

Contact Information

MolSoft, LLC 3366 North Torrey Pines Court, Suite 300 La Jolla CA 92037 www.molsoft.com

Prof. Ruben Abagyan, MolSoft Founder Telephone: (858) 625-2000, ext 105 abagyan@gmail.com

Andrew Orry, PhD, Senior Research Scientist Telephone: (858) 625-2000, ext 108 andy@molsoft.com

Crystal Crawford, MolSoft, General Counsel Telephone: (858) 625-2000, ext 102 crystal@molsoft.com