Review for "An explicit-solvent conformation search method using open software"

Completed on 13 Apr 2016 by Timothy Plageman.

License: http://creativecommons.org/licenses/by/4.0/

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Comments to author

Basic reporting

see below

Experimental design

see below

Validity of the findings

see below

Comments for the author

In my opinion the following issues should be addressed before the paper is suitable for publication

  1. The following Information needs to be provided (as text files on, e.g. Figshare ) for reproducibility: a. The smiles strings used for Amanitin and Cabergoline. b. Start coordinates used for simulations c. Coordinates for the structures shown in Figures 4 and 5 d. In addition, the authors should describe the protonation state they used for Cabergoline

  2. The authors may want to note in the manuscript (warn the reader) that Babel smiles conversion can produce the wrong stereo isomers for chiral centers in fused rings.

  3. a. The authors may want to note that their scheme identifies the lowest free energy conformer rather than the lowest potential energy conformer (which is what oBabel and related methods do). B. related to this, a discussion of whether the simulation is run sufficiently long to yield meaningful free energy differences would be useful

  4. In the Solvation of Solute subsection the authors mention the generation of CHARMM-format parameters, but later write “The potential energy terms for the solute were described using the General Amber Force Field (GAFF).” This was confusing to me and the authors should clarify.

  5. Cabergoline contains two tertiary amines which represent particular challenges for conformational searches since they, in effect, are chiral centers and inversion is not considered a degree of freedom in the oBabel conformer search when these N atoms are in a ring. The starting “chirality” of these centers in the starting structure is thus more or less arbitrary. Furthermore, if the N is protonated this degree is certainly not sampled in the MD as it would effectively require deprotonation. For deprotonated centers it is also not obvious that the inversion barrier is low enough to allow this degree of freedom to be sampled. The authors should discuss this point.

Regards,

The PeerJ Team peerj.com