3 papers
q-bio.QM2024
Chemistry-informed Machine Learning Explains Calcium-binding Proteins Fuzzy Shape for Communicating Changes in the Atomic States of Calcium Ions
Pengzhi Zhang, Jules Nde, Yossi Eliaz +3
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination…
cond-mat.mtrl-sci2021
CTRAMER: An open source software package for correlating interfacial charge transfer rate constants with donor acceptor geometries in organic photovoltaic materials
Jacob Tinnin, Huseyin Aksu, Zhengqing Tong +5
In this paper we present CTRAMER (Charge Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory), an open source software package for calculating interfacial…
q-bio.BM2020
Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif
Pengzhi Zhang, Jaebeom Han, Piotr Cieplak +1
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding a…