The 2013 Nobel Laureates in Chemistry Shneior Lifson's 100Th

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The 2013 Nobel Laureates in Chemistry Shneior Lifson's 100Th

The Faculty of Chemistry COMMEMORATING Shneior Lifson's 100th Birthday HONORING The 2013 Nobel Laureates in Chemistry May 12, 2014 Ebner Auditorium, Weizmann Institute of Science 9:00-9:30 Coffee 9:30-9:40 Daniel Zajfman, President of the Weizmann Institute 9:40-9:50 Gilad Haran, Dean of the Faculty of Chemistry, Weizmann Institute 9:50-10:25 Arieh Warshel, 2013 Nobel prize laureate, Univ of Southern California Multiscale Modeling of Biological Systems and Processes 10:25-11:00 Buzz Baldwin, Stanford Univ The Basis of the Hydrophobic Effect: a Hydration Shell Formed by van der Waals Attraction 11:00-11:15 Coffee break Chair: Amnon Horovitz, Weizmann Institute of Science 11:15-11:50 Johan Aqvist, Uppsala Univ Optimization of Thermodynamic Activation Parameters in Enzyme Catalysis 11:50-12:25 Shoshana Wodak, Univ of Toronto Protein Interactions, Short Stories 12:25-13:00 Lewis Kay, Univ of Toronto Towards a New Paradigm in Structural Biology: Atomic Resolution Studies of Conformationally Excited Protein States 13:00-14:00 Lunch break Chair: Gideon Schreiber, Weizmann Institute of Science 14:00-14:35 Elisha Haas, Bar-Ilan Univ Folding and Dynamics of Protein Molecules 14:35-15:10 Elliot Elson, Washnigton Univ Relaxation Kinetics of Cellular Metabolic Steady States 15:10-15:25 Coffee break Chair: Deborah Fass, Weizmann Institute of Science 15:25-16:00 Vijay Pande, Stanford Univ Some Surprises in the Biophysics of Protein Dynamics: Simulating Conformation Change of Kinases and GPCRs with Folding@home 16:00-16:35 Michael Levitt, 2013 Nobel prize laureate, Stanford Univ Birth and Future of Multi-Scale Modeling for Macromolecular Systems 16:35-16:40 Koby Levy, Weizmann Institute of Scienc Closing Remarks Sponsors • The Lifson Family • The Clore Center for Biological Physics For more information REGISTRATION • The Goldschleger Foundation [email protected] Registration is free but required.

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FF12MC: a Revised AMBER Forcefield and New Protein Simulation Protocol
bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. FF12MC: A revised AMBER forcefield and new protein simulation protocol Yuan-Ping Pang Computer-Aided Molecular Design Laboratory, Mayo Clinic, Rochester, MN 55905, USA Corresponding author: Stabile 12-26, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA; E-mail address: [email protected] Short title: FF12MC: A new protein simulation protocol Keywords: Protein folding; Protein dynamics; Protein simulation; Protein structure refinement; Molecular dynamics simulation; Force field; Chignolin; CLN025; Trp-cage; BPTI. bioRxiv preprint doi: https://doi.org/10.1101/061184; this version posted July 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. ABSTRACT Specialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened C– H bonds, (ii) removal of torsions involving a nonperipheral sp3 atom, and (iii) reduced 1–4 interaction scaling
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