Enzyme Design

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

I've been running several rounds of RosettaMatch lately and I'd like them to go faster. I'm pretty sure writing matches is the part slowing it down. Is there anyway to limit the number of matches it outputs? For example, for the same matched sequence (say H133H135H432), I get anywhere from 50-400 cloudPDB files. I don't want more than the first one or two, because the rest are almost always just different ligand positions and I'll end up running EnzDesign anyways. I'm using these flags:

Hey everyone,

I am trying to design a protein with a covalent bond between the C of Thr and the N of Gly with a Tyr in between them (imitating the chromophore from GFP for perspective). Because of this odd 5-membered ring formation, I used Thr/Gly with a generous distance constraint between them in my CST file when I ran RosettaMatch to find likely sites in my scaffold proteins. My sites place the two backbone atoms ~4-5A apart.

I am working on developing my CST file for the protein I'm designing and I have a few questions about some of the additional constraints I've seen in the example CSTs mentioned in the user's manual.