In this paper we examine how the lactose permease, LacY, changes its structure to shuttle molecules of lactose across a cell membrane. The change in conformation is modelled usinga biased computational method called dynamic importance sampling (DIMS) and the results compared to the results of some previously published double electron electron spin resonance (DEER) experiments. […]
Can we predict the conductance of a potassium ion channel from an experimental structure? In this paper we examine the kinetic barriers experienced by potassium ions (and waters) as they move through the narrowest part of two different potassium ion channels. We examine the reproducibility of our results and test the sensitivity of the approach to […]
So if I have a particular system I want to simulate, how many processing cores can I harness to run a single GROMACS version 4.6 job? If I only use a few then the simulation will take a long time to finish, if I use too many the cores will end up waiting for communications […]
GROMACS is a scientific code designed to simulate the dynamics of small boxes of stuff, that usually contain a protein, water, perhaps a lipid bilayer and a range of other molecules depending on the study. It assumes that all the atoms can be represented as points with a mass and an electrical charge and that all […]
Crowd-sourced computer networks Blog post on something I’ve been interested in for a while; how to create and use networks of everyday computers to solve interesting problems in biology. Links to the website of the Software Sustainability Institute.
What can we learn using computational methods about how potassium ions and water molecules move through the narrowest part of a potassium channel? In this paper, we calculate the average force experienced by three potassium ions as they move through the selectivity filter of a voltage-gated potassium channel. This allows us to identify the most probably mechanism, […]