Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems
2015 (English)In: Journal of Molecular Graphics and Modelling, ISSN 1093-3263, E-ISSN 1873-4243, Vol. 60, 15-23 p.Article in journal (Refereed) Published
Structural information and activity data has increased rapidly for many protein targets during the last decades. In this paper, we present a high-throughput interface (Qgui) for automated free energy and empirical valence bond (EVB) calculations that use molecular dynamics (MD) simulations for conformational sampling. Applications to ligand binding using both the linear interaction energy (LIE) method and the free energy perturbation (FEP) technique are given using the estrogen receptor (ER alpha) as a model system. Examples of free energy profiles obtained using the EVB method for the rate-limiting step of the enzymatic reaction catalyzed by trypsin are also shown. In addition, we present calculation of high-precision Arrhenius plots to obtain the thermodynamic activation enthalpy and entropy with Qgui from running a large number of EVB simulations.
Place, publisher, year, edition, pages
2015. Vol. 60, 15-23 p.
Thermodynamic activation parameters, Free energies, Q, Empirical valence bond, Linear interaction energy, Molecular dynamics, Free energy perturbation
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:uu:diva-261316DOI: 10.1016/j.jmgm.2015.05.007ISI: 000359174900002PubMedID: 26080356OAI: oai:DiVA.org:uu-261316DiVA: diva2:851013