"Freely Available Conformer Generation Methods: How Good Are They?" J Chem Inf Model 2012, 52 (5), 1146–1158. There are a few benchmark papers - largely grabbing a few conformers, usually including a mix of free or open source tools and commercial tools. Most people usually mean 'close to the experimental crystal structure' which is not usually the same as 'lowest energy'. I'm not sure there are many papers on the first (i.e., generate one 3D structure - how good is it)? For one, it would depend a lot on your definition of 'good.' I personally prefer 'low energy conformer' because it's easy to define. The trick is that there's a fine distinction between "generating 3D coordinates" (i.e., one conformation) and "generating 3D coordinates and doing some conformer sampling" presumably with the latter helping to find a low-energy conformer, thermally-accessible ensemble, or a pose that might match an experimental structure or drug docking pose. This is an interesting question, since a reviewer just asked us to do such a benchmark. Summary: RDKit ETKDG is currently the best open source tool (Survey papers that have previously done comparisons of this sort would also be welcome and appreciated, so that I can see what hasn't already been covered by previous researchers.)
#Pymol free version windows 2019 software
I am already using OpenBabel and RDKit to generate coordinates, so I got the idea to look for other software to compare with it. If there is no such list, would you be able to recommend any software for this task?
I was envisioning doing tests for at least those formats, unless I am missing anything.
I am not expecting the software to handle oligopeptides or other sizable biomolecules). I was able to settle on the following constraints: freely available, or at least free for academic users can be run on the command line (either Windows or *nix) and, can handle small to medium-sized molecules (I.e. Is there a list anywhere of chemical software that does this? As part of some research I am doing, I want to do a head-to-head comparison of software for generating 3D atomic coordinates for molecules.
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