Bennett McIntosh Adademy of the sciences of the Czech Republic Department of structure and Function of Proteins Nové Hrady, South Bohemia, Czech Republic

Solving protein structures computationally Most of EcoR124I structure known previously New domain partially solved by intern last year Used MD (Molecular Dynamics) engine gromacs and geometric tool concoord to narrow possibilities

concoord & gromacs GROMACS CONCOORD Simulates protein in water Numerical technique: each frame represents 2 quadrillionths of a second, and is derived from the position, speed and force in the previous frame. Shows how stable candi- date structure is. Finds possible protein shapes Used to find structures which can arrange themselves as seen in previous crystal structures Right de Groot BL, et al (1997); Left https://www.princeton.edu/researchcomputing/computational-hardware/machine-2/

Results & Impact Scientific Results: One structure found which was stable for the first 90 links of the 120-link chain we were looking at (green box) but unstable in the last 30 (red box)

Results & Impact CONCOORD protocol Developed protocol for using the CONCOORD tool to verify possible structures found using GROMACS tool.

Regional and global connections I was able to meet and interact with scientists in the field from all of these cities, learning their approach to research and science. Meeting scientists from all over Europe, some of whom may advise my spring independent work

Regional and global connections Celebrating the 4th of July with scientists from 5 continents

Conferences & classes in Nové Hrady In addition to the conferences, I was able to learn experimental techniques for studying proteins, giving me skill beyond the immediate project. Learning scientific methods from experts in the field

Travelling about Central Europe during the peak of World Cup season Travel and awareness Travelling about Central Europe during the peak of World Cup season Experiencing history in the castles, towns and churches where it happened