Exploring Protein Folding Space with Neural Network Guided Simulations

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KŘENEK Aleš HOZZOVÁ Jana OĽHA Jaroslav TRAPL Dalibor SPIWOK Vojtěch

Year of publication 2020
Type Article in Proceedings
MU Faculty or unit

Institute of Computer Science

Web program konference
Keywords metadyamic; protein folding; netural network
Description We introduce a novel computationally feasible method of exploring protein folding spaces, while working with- out any a priori knowledge of the space, hence over- coming a drawback of previous methods. Since our ap- proach uses random landmark structures without any guarantee of chemical or biological meaning, we use neu- ral networks to extract meaningful features to guide the simulation. The method is described in detail, and its implementation is publicly available. We demonstrate the feasibility of this approach by accelerating the fold- ing of the Trp-Cage miniprotein 20 times.
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