CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

K Vanommeslaeghe, AD MacKerell Jr - Biochimica et Biophysica Acta (BBA …, 2015 - Elsevier
Abstract Background Molecular Mechanics (MM) is the method of choice for computational
studies of biomolecular systems owing to its modest computational cost, which makes it …

Lipid nanotechnology

S Mashaghi, T Jadidi, G Koenderink… - International journal of …, 2013 - mdpi.com
Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices
and machines derived from engineering, physics, materials science, chemistry and biology …

Lipid14: the amber lipid force field

CJ Dickson, BD Madej, ÅA Skjevik… - Journal of chemical …, 2014 - ACS Publications
The AMBER lipid force field has been updated to create Lipid14, allowing tensionless
simulation of a number of lipid types with the AMBER MD package. The modular nature of …

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

JB Klauda, RM Venable, JA Freites… - The journal of …, 2010 - ACS Publications
A significant modification to the additive all-atom CHARMM lipid force field (FF) is developed
and applied to phospholipid bilayers with both choline and ethanolamine containing head …

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes

S Jo, JB Lim, JB Klauda, W Im - Biophysical journal, 2009 - cell.com
Abstract The CHARMM-GUI Membrane Builder (http://www. charmm-gui.
org/input/membrane), an intuitive, straightforward, web-based graphical user interface, was …

Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids

JPM Jämbeck, AP Lyubartsev - The journal of physical chemistry …, 2012 - ACS Publications
An all-atomistic force field (FF) has been developed for fully saturated phospholipids. The
parametrization has been largely based on high-level ab initio calculations in order to keep …

An extension and further validation of an all-atomistic force field for biological membranes

JPM Jambeck, AP Lyubartsev - Journal of chemical theory and …, 2012 - ACS Publications
Biological membranes are versatile in composition and host intriguing molecular processes.
In order to be able to study these systems, an accurate model Hamiltonian or force field (FF) …

A new force field for simulating phosphatidylcholine bilayers

D Poger, WF Van Gunsteren… - Journal of computational …, 2010 - Wiley Online Library
A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid‐
crystalline, fluid phase at zero surface tension is presented. The structure of the bilayer with …

Another piece of the membrane puzzle: extending slipids further

JPM Jambeck, AP Lyubartsev - Journal of chemical theory and …, 2013 - ACS Publications
To be able to model complex biological membranes in a more realistic manner, the force
field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin …

On the Validation of Molecular Dynamics Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment

D Poger, AE Mark - Journal of Chemical Theory and Computation, 2010 - ACS Publications
Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied
phospholipids, 1, 2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1, 2-dimyristoyl-sn …