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CANCELLED: TYC Seminar: What can CHARMM-GUI do for you?
Wonpil Im. Soyeon Yoo – Lehigh University
Venue: Physics E7 – Grd Floor, Physics Building, UCL
20 October 2023 @ 3:00 pm – 4:30 pm
Abstract: Since its original development in 2006, CHARMM-GUI has proven to be an ideal web-based platform to interactively build complex molecular systems and prepare their simulation inputs with well-established and reproducible simulation protocols for state-of-the-art molecular simulations using widely used simulation packages. The CHARMM-GUI development project has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of molecular simulation systems. Our philosophy in CHARMM-GUI development is less about providing the nuts and bolts of molecular modeling, but instead focused on helping users to achieve a task, such as building a membrane system or solvating a protein, by providing a streamlined interface. This design principle helps us to think of the workflow critically when designing the interface, which leads CHARMM-GUI to be accessible to users with little experience in modeling tools and remains useful to experts, especially for batch generation of systems. The CHARMM-GUI development project is still ongoing. CHARMM-GUI will continue to help expert and non-expert researchers from a broader range of the modeling and simulation community to build the complex molecular systems of their interest and prepare the input files for any general and advanced modeling and simulation through the large and unique scope of CHARMM-GUI functionality, allowing the research community to carry out innovative and novel molecular modeling and simulation research. In this talk, I will present the past, present, and future of the CHARMM-GUI development project, and some applications for specific modules will be also discussed.
Bio: Wonpil Im received in bachelor’s and master’s degrees from Hanyang University in Seoul. He then earned his Ph.D. in Biochemistry from Cornell University. He did his post-doctoral research at the Scripps Research Institute in La Jolla, California. In 2005, he was hired as an assistant professor in the Center for Computational Biology and Department of Molecular Biosciences at the University of Kansas, Lawrence. In 2011, he was promoted to associate professor and then professor in 2015. In 2016, he joined the Faculty in Departments of Biological Sciences and Bioengineering at Lehigh University, and he has been named the Presidential Endowed Chair in Health – Science and Engineering. Wonpil was awarded the Alfred P. Sloan Research Fellowship (2007), ACS HP Outstanding Junior Faculty Award (2011), J. Michael Young Undergrad Advisor Award (2011), Meredith Docking Scholar (2013), and University Scholarly Achievement Award (2015). the Friedrich Wilhelm Bessel Research Award from the Humboldt Foundation (2017), Lehigh CAS Dean’s Research Award (2019), Libsch Research Award (2021), and was named a KIAS Scholar from the Korea Institute for Advanced Study (2016).
Research in his lab is focused on the applications of theoretical/computational methods to chemical and physical problems in biology and material sciences. In particular, he is interested in modeling and simulations of biological membranes and associated proteins, glycoconjugates, and protein-ligand (drug) interactions. In addition, his lab has been developing CHARMM-GUI for the biomolecular modeling and simulation community.