More citations for membrane protein embedding algorithms - Redmine #1932
Archive from user: Semen Yesylevskyy
An algorithm of embedding proteins into the membranes, which is now integrated into mdrun, comes from the paper of Wolf et al, J Comp Chem 31 (2010) 2169-2174.
However, this algorithm of squeezing protein and growing it back in the membrane was proposed by us much earlier in 2007:
S.O. Yesylevskyy, “ProtSqueeze: simple and effective automated tool for setting up membrane protein simulations”, Journal of chemical information and modeling 47 (5), 1986-1994.
The paper of Wolf gives no credit to our work, while the algorithm is essentially the same. I already sent a request to the authors of Wolf’s paper concerning possible violation of scientific ethics in this case.
Taking into account wide spread of this methodology provided by Gromacs, the question of priority becomes sensible.
The manual should mention both works. Our work should be mentioned as the first publication of “squeezing-growing” algorithm. The works of Wolf should be mentioned as an implementation of this algorithm, which is used in mdrun.
(from redmine: issue id 1932, created on 2016-03-29 by gmxdefault, closed on 2016-06-23)
- Revision ea690f00 by Semen Yesylevskyy on 2016-06-07T13:40:23Z:
Added manual section about embedding proteins to membranes. Very short paragraph referencing needed papers and linking to user guide for details. Fixes #1932 Change-Id: I0511576f06be35f1727a22c0d1e5f6552f1ae06d