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Enzyme Design

Altering substrate specificity

Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

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.

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RosettaMatch outputs

Category: 
Design
Enzyme Design

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:

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Enzyme Design with additional covalent backbone bonds

Category: 
Design
Enzyme Design
Constraints
Non-Canonical Peptides

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.

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Convert Rotamer Vector to Chi Angles

Category: 
Enzyme Design

Dear PyRosetta Community,

I am attempting to find the closest rotamer to each residue in a protein and then obtain the chi angles for each of those closest rotamers. I have successfully used the core.pack.dunbrack.rotamer_from_chi function to obtain the rotamer vector, thanks to the topic "Rotamer information from pose." Is there a reverse function, essentially "chi_from_rotamer," that will return the chi angles that correspond to the rotamer vector that rotamer_from_chi yields?

Thank you.

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Files for Spatial Constraints

Category: 
Structure prediction
Enzyme Design
Constraints

Hi guys,

I am trying to locate the files to generate spatial constraints from homologous template structures for comparative modelling as given in the Thompson and Baker paper from 2011. I can't find them anywhere in the ROSETTA directories. Are they available anywhere?

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Running the Matcher on multiple PDBs

Category: 
Enzyme Design

I'm having issues getting the Matcher to run. My .flags file looks like this (file names changed):

-s PDB1.pdb

-s PDB2.pdb

-match:lig_name LIG

-match:scaffold_active_site_residues POS.pos

-match:geometric_constraint_file CST.cst

-extra_res_fa PARAM.params

-ex1

-ex2

-use_input_sc

Both PDBs are in the same directory, and the Matcher runs fine in that it will get a number of matches for PDB1.pdb, but then it just ends... see:

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