Quantification and visualization of molecular surface flexibility |
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| Affiliation: | 1. Institute of Electrical Engineering, Yanshan University, Qinhuangdao 066004, PR China;2. School of Electrical and Data Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia;1. Department of Forest Economics, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden;2. Center for Environmental and Resource Economics, CERE, Umeå, Sweden;3. Umeå School of Business and Economics (USBE), Department of Economics, Umeå University, Umeå, Sweden;4. Finnish Meteorological Institute, Helsinki, Finland;5. Department of Economics, Oulu Business School, Oulu University, Finland;1. StreamNovation Ltd., H-1083, Budapest, Práter utca 50/a., Hungary;2. Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, H-1083, Budapest, Práter utca 50/a., Hungary |
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| Abstract: | Two new methods for the quantification and visualization of the flexibility of molecular surfaces are presented. Both methods rely on results of molecular dynamics (MD) simulations. Whereas method I is based on a simple but fast grid-counting algorithm, method II uses a mapping function that allows for a sharp and clear visualization of atomic RMS fluctuations on a molecular surface. To demonstrate the scope of the methods, MD simulations of two proteins, PTI and ubiquitin, were performed. The flexibility data are mapped onto the molecular surfaces of the proteins and visualized using texture mapping technology available on modern workstations. |
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