Browsing by Author "Polêto, Marcelo D."

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    Integration of experimental data and use of automated fitting methods in developing protein force fields
    Polêto, Marcelo D.; Lemkul, Justin A. (Springer Nature, 2022-03-18)
    The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergence of polarizable force fields and the role of electronic polarization and areas in which additive force fields fall short. The use of automated fitting methods and the inclusion of additional experimental solution data during parametrization is discussed as a means to highlight possible routes to improve the accuracy of force fields even further.
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    TUPÃ: Electric field analyses for molecular simulations
    Polêto, Marcelo D.; Lemkul, Justin A. (Wiley, 2022-04-22)
    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 at https://mdpoleto.github.io/tupa/.