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Title: Computing Protein pKas Using the TABI Poisson–Boltzmann Solver
• To compute protein pKas, a continuum dielectric Poisson-Boltzmann model defined on a molecular domain and a solvent domain is used for computing the related electrostatic free energies (top left). • The PB model in its boundary integral form is accurately solved on the triangulated molecular surface (e.g. BPTI) accelerated by a fast Treecode algorithm (top right). • The method obtains the intrinsic pKa and then computes the protonation probability for a given pH including site-site interactions by going through an energy driven titrating procedure. Comparison with experimental results are provided (bottom left and right).  more » « less
Award ID(s):
1819094 1819193
NSF-PAR ID:
10249378
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
Journal of Computational Biophysics and Chemistry
Volume:
20
Issue:
02
ISSN:
2737-4165
Page Range / eLocation ID:
175 to 187
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    How were predictions validated?

    Please see

    Weinstein, B. G., Marconi, S., Bohlman, S. A., Zare, A., & White, E. P. (2020). Cross-site learning in deep learning RGB tree crown detection. Ecological Informatics56, 101061.

    Weinstein, B., Marconi, S., Aubry-Kientz, M., Vincent, G., Senyondo, H., & White, E. (2020). DeepForest: A Python package for RGB deep learning tree crown delineation. bioRxiv.

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