Mohammad Mehdi Ghahremanpour1, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel. 1. Department of Bioinformatics, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran, School of Mathematics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Computer Science, Faculty of Engineering, University of Tehran, Tehran, Iran, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden and Department of Chemistry, Zhejiang University, Hangzhou 310027, China.
Abstract
MOTIVATION: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations. RESULTS: To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface. AVAILABILITY AND IMPLEMENTATION: MemBuilder is a free web server available from www.membuilder.org.
MOTIVATION: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations. RESULTS: To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface. AVAILABILITY AND IMPLEMENTATION: MemBuilder is a free web server available from www.membuilder.org.
Authors: William G Glass; Jonathan W Essex; Franca Fraternali; James Gebbie-Rayet; Irene Marzuoli; Marley L Samways; Philip C Biggin; Syma Khalid Journal: Methods Mol Biol Date: 2021
Authors: Sunhwan Jo; Xi Cheng; Shahidul M Islam; Lei Huang; Huan Rui; Allen Zhu; Hui Sun Lee; Yifei Qi; Wei Han; Kenno Vanommeslaeghe; Alexander D MacKerell; Benoît Roux; Wonpil Im Journal: Adv Protein Chem Struct Biol Date: 2014-08-24 Impact factor: 3.507