Virtual environment for studying the docking interactions of rigid biomolecules with haptics

Haptic technology facilitates user interaction with the virtual world via the sense of touch. In molecular docking, haptics enables the user to sense the interaction forces during the docking process. Here we describe a haptics-assisted interactive software tool, called Haptimol RD, for the study of docking interactions. By utilising GPU-accelerated proximity querying methods very large systems can now be studied. Methods for force scaling, multipoint collision response and haptic navigation are described that address force stability issues that are particular to the interactive docking of large systems. Thus Haptimol RD expands, for the first time, the use of interactive biomolecular haptics to the study of protein-protein interactions. Unlike existing approaches, Haptimol RD is designed to run on relatively inexpensive consumer-level hardware and is freely available to the community

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Virtual reality computer program for biomolecule structure determination

Protein structures are complex 3-dimensional shapes that are experimentally determined using x-ray crystallography and cryogenic electron microscopy. Interpreting the data that these methods yield involves building simplified 3D models. Some portion of time spent creating these models must be spent manually modifying the model in order to make it line up with the data; this is difficult and time consuming, in part because the data is “blurry” in three dimensions. We have created a computer program for performing this task in virtual reality, which allows structural biologists to build models using their hands. Furthermore, we have evaluated the program and found that it speeds up model building, in certain circumstances