I have a structure of a peptide we are working with (not yet on rcsb.org, but will be eventually). We have a quite large number of analogs that we want to model the structures of to use with Haddock (https://wenmr.science.uu.nl/haddock2.4/).
My first thought was to use Modeller (https://salilab.org/modeller/). The problem is that we have many non-standard amino acids that are not supported. This is things like D-amino acids (very important to get right), hydroxyprolines (fairly important to get right), gamma-carboxyglutamates (potentially less important), and a few others that we think are less important for function (more for stability).
Are there any good alternatives, that can work with non-standard amino acids? At the very least, D-amino acids, but preferably also at least hydroxyprolines.
Hi,
CHARMM-GUI have a good database of modified aminoacids, you can check that. Or you can build all your custom residues in AMBER. There are a few tutorials on how to do that (you can virtually build anything):
https://ambermd.org/tutorials/basic/tutorial5/index.php
Check https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007449
Check https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/protein-structure-prediction
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