TUPÃ: Electric field analyses for molecular simulations
- 22 April 2022
- journal article
- research article
- Published by Wiley in Journal of Computational Chemistry
- Vol. 43 (16) , 1113-1119
Abstract
We introduce TUPÃ, a Python‐based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained athttps://mdpoleto.github.io/tupa/.Keywords
Funding Information
- National Institute of Food and Agriculture (VA‐160092)
- National Institute of General Medical Sciences (R35GM133754)
This publication has 42 references indexed in Scilit:
- Polarizable Atomic Multipole-Based AMOEBA Force Field for ProteinsJournal of Chemical Theory and Computation, 2013
- Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and ModulationFrontiers in Pharmacology, 2012
- Factors determining electrostatic fields in molecular dynamics simulations of the ras/effector interfaceProteins: Structure, Function, and Bioinformatics, 2011
- MDAnalysis: A toolkit for the analysis of molecular dynamics simulationsJournal of Computational Chemistry, 2011
- Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sitesProceedings of the National Academy of Sciences, 2010
- Nitrile Bonds as Infrared Probes of Electrostatics in Ribonuclease SThe Journal of Physical Chemistry B, 2010
- Current Status of the AMOEBA Polarizable Force FieldThe Journal of Physical Chemistry B, 2010
- CHARMM: The biomolecular simulation programJournal of Computational Chemistry, 2009
- Electrostatic Basis for Enzyme CatalysisChemical Reviews, 2006
- A polarizable model of water for molecular dynamics simulations of biomoleculesChemical Physics Letters, 2006