PypKa: A Flexible Python Module for Poisson–Boltzmann-Based p<i>K</i><sub>a</sub> Calculations
Pedro B. P. S. Reis, Diogo Vila‐Viçosa, Walter Rocchia, Miguel Machuqueiro
Abstract
calculations in existing protocols with the addition of a few extra lines of code. PypKa supports CPU parallel computing on solvated proteins obtained from the PDB repository but also from MD simulations using three common naming schemes: GROMOS, AMBER, and CHARMM. The code and documentation to this open-source project is publicly available at https://github.com/mms-fcul/PypKa.
Topics & Concepts
Python (programming language)Poisson distributionComputer sciencePhysicsProgramming languageMathematicsStatistical physicsStatisticsNanopore and Nanochannel Transport StudiesAdvanced Thermodynamics and Statistical MechanicsElectrostatics and Colloid Interactions