Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.
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ABSTRACT:
SUBMITTER: Kekenes-Huskey PM
PROVIDER: S-EPMC3535444 | biostudies-literature | 2012 Oct
REPOSITORIES: biostudies-literature
Publications
Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.
Kekenes-Huskey P M PM Gillette A A Hake J J McCammon J A JA
Computational science & discovery 20121001
We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C a ...[more]
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