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- W1975120703 abstract "Protein folding simulations have the potential to help us figure out the problem of protein folding. However, the highly frustrated energy landscapes of protein folding limits the use of these techniques. Hence, many new algorithms are developed each year aiming at improving sampling efficiency, producing results in shorter times. We have developed and tested an algorithm using GPU technology that allows us to fold several proteins within weeks of computational usage.Our work extends on the principles of protein folding through zipping and assembly. In this view, local events such as helix formation happen first (zipping), and non-local ones later (assembly). The assembly step is slow: in order to form native like contacts the residues involved have to first find each other. Our algorithm takes advantage of the fact that proteins form hydrophobic cores to guide the assembly step. We accelerate the process by adding restraints in our simulations that brings pairs of hydrophobic residues together, favoring the formation of native-like contacts. Since not all hydrophobic pairs will lead to native-like contacts we use a Hamiltonian and Temperature Replica exchange algorithm (H,T-REMD), that allows us to modulate the strengths of these restraints. Thus, the restraints that the underlying molecular force field favors are enforced, where as the ones that are not favored are turned off.This method allows us to jump between different sets of contacts easily, sampling many different topologies and limiting the amount of sampling that is required in between. In this way we have been able to get native-like structures for a small set of proteins. During my presentation I will show how the method works and how successful it is in a small set of proteins." @default.
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- W1975120703 date "2014-01-01" @default.
- W1975120703 modified "2023-09-30" @default.
- W1975120703 title "Hydophobic Guided Protein Folding" @default.
- W1975120703 doi "https://doi.org/10.1016/j.bpj.2013.11.2466" @default.
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