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made with VMD
Sunlight powers life on Earth. This basic fact has been known since ancient times and retold many times in many cultures. Today, scientists understand the means through which light powers life at atomistic detail, as a chain of processes climbing scales from electronic interactions to cooperation between proteins to cell-scale integration of energy conversion. These processes have been illustrated in a recent video that was awarded the BEST SCIENTIFIC VISUALIZATION OF 2019 at the SC19 conference, Scientific Visualization & Data Analytics Showcase. The video is a joint production with the team of Donna Cox at NCSA and is based on a decade long collaborative effort with the experimental group of Neil Hunter and a lifetime research interest for Klaus Schulten. The underlying scientific investigation illustrated in the video was presented in 18 manuscripts over the past decade, from atomic scale structural modeling to organelle-scale and cell-scale integration of function. These modeling efforts also led to a molecular dynamics simulation of the chromatophore using NAMD, recently published in Cell. The video segment, produced with VMD, that won as the Best Scientific Visualization is an excerpt from the fulldome movie 'Birth of Planet Earth' released to planetariums worldwide by Spitz Creative Media. The oldest story of humanity — light powering life — coming soon to a theater near you.
made with VMD
Neurotransmitters are chemical messengers diffusing across the synapse to propagate nerve impulses. The serotonin transporter (SERT) is a protein embedded in the cellular membrane of the pre-synaptic neuron, which recycles the neurotransmitter serotonin. It plays pivotal roles in modulating behavior, rendering it a primary drug target for neuropsychiatric disease. Inhibition of the serotonin uptake by SERT contributes to the mechanism of clinically used antidepressants. To provide structural insights into the transport mechanism, our collaborators in the Gouaux lab (OHSU) captured a series of structures of SERT in multiple functional states using cryoEM. The structures were co-crystalized with an inhibitor, ibogaine, a hallucinogenic drug found in plants with anti-addictive potential, in the substrate-binding pocket. However, the exact binding poses of ibogaine in these structures remained ambiguous due to the limited resolution, prohibiting a direct interpretation of ibogaine's inhibition mechanism. To settle this problem, we developed a computational docking approach to systematically search for the most probable ibogaine binding poses, which best fit into the experimental density maps and exhibit considerable stability in the following by molecular dynamics simulations performed with NAMD. Read more in Nature.
Modern molecular simulation, visualization, and modeling techniques often require high-performance computing hardware to obtain the best efficiency. However, access to such hardware can be a barrier for some researchers. As an alternative, cloud computing provides a cost-effective and practical solution for many molecular modeling tasks and for small and moderate size molecular dynamics simulations. The cloud computing model provides researchers with access to powerful computational equipment that would otherwise be too costly to procure, maintain, and administer on their own. Additionally, cloud platforms can easily bundle different software packages used in a modeling workflow to guaruntee their availablity and interoperability on a standardized system. We have adapted our molecular modeling applications NAMD, VMD, and associated tools to operate within the Amazon Web Services (AWS) Elastic Compute Cloud (EC2) platform, enabling popular research workflows to be run remotely by scientists all over the globe, with no need for investment in local computing resources and a reduced requirement for expertise in high performance computing technologies. Recent advancements in GPU virtualization technology now make it possible to use cloud computing for large-scale scientific computing, data analysis, and visualization tasks. The latest release of our cloud software can be run on EC2's latest graphics hardware, backed by DCV, to provide a smooth and seamless graphical working environment. Instance types specially designed for parallel CPU or GPU workloads provide users with access to the hardware they need to run even the most demanding features of NAMD and VMD, all from their much less powerful personal computers and even laptops. These instances can be paid for on an on-demand, as-needed basis, and some workflows, such as Molecular Dynamics Flexible Fitting, can be run for less than the cost of a cup of coffee. Our cloud virtual machine image is availble in the Amazon Marketplace, which provides users with a very simple one-click launch using pre-configured choices of instance types that have been tested with our software. To learn more, see our cloud research page.