Abstract
Motivation Polypeptide sequence length is the single dominant factor hampering the effectiveness of currently available software tools for de novo calculation of amino acid-specific protonation constants in disordered polypeptides. Results We have developed pepKalc, a robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded states. Our software completely removes the limitations of the previously reported Monte-Carlo approaches in the computation of protein electrostatics by using a hybrid approach that effectively combines exact and mean-field calculations to rapidly obtain accurate results. Paired with a modern architecture GPU, pepKalc is capable of evaluating protonation behavior for an arbitrary-size polypeptide in a sub-second time regime.
Originalsprog | Engelsk |
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Tidsskrift | Bioinformatics |
Vol/bind | 34 |
Nummer | 12 |
Sider (fra-til) | 2053-2060 |
Antal sider | 8 |
ISSN | 1367-4803 |
DOI | |
Status | Udgivet - 15 jun. 2018 |