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Abstract
摘要 |
Simulation of large biomolecules and biomolecular complexes is still an open challenge especially when interested large scale and long time phenomena such as the folding of proteins and RNA. Atomistic simulations are limited to small systems and to short time scales even when adopting the most advanced computer technologies and sampling strategies. We have developed two coarse-grained models, OPEP for proteins and HiRE-RNA for nucleic acids, that have proven effective to study folding, aggregation and assembly of peptides, RNA and DNA. I will present the models, explain their forcefields, and the state-of-the art enhanced sampling techniques used for simulation. I will present examples of the studies possible with these methods on large systems. When available, integrating experimental data into the simulation protocol greatly reduces the conformational space to be explored and leads to faster convergence to data-compatible structures. I will discuss how we can integrate various sources of experimental data into our models and I will conclude with the presentation of our most recent work on an interactive simulations software explicitly designed for the use by experimentalists. |
