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what factors determine the lowest (best) LigInterfaceEnergy score?

Submitted by jmaly on Wed, 2020-08-26 13:07
Category: 
Docking
Scoring
Small Molecules

Hi everyone.

We are docking small molecule ligands into non-enzyme proteins to get an idea of ligand distribution/convergence within the binding pocket, using the LigInterfaceEnergy mover. While the results are promising, ligands with the lowest LigInterface energy are sometimes outliers within the ligand distribution. There is no native structure to compare to other than the input pose.

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Rosetta 3 - General

I made a RDKit Chem.Mol to params converter — feedback welcome!

Submitted by matteoferla on Sun, 2020-05-03 10:14
Category: 
Small Molecules

For a project I was really in need of a clean way to convert a RDKit Chem.Mol object to a params file as the way I was making params files was horrid.

So I ended up writing a MIT-licenced python module that can load and save params files and do "surgery" on them or create one from a RDKit Mol object, which can include the dummy atom (*) which becomes a connect entry. It can be used without either rdkit installed (surgery only!) or pyrosetta installed (no testing method).

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Rosetta 3 - General

Ligand docking at specific orientation

Submitted by ShiranBZ on Mon, 2020-04-13 20:46
Category: 
Small Molecules

Hi all,

I am trying to use RosettaLigand to dock a rod-shaped molecule into a protein binder with a deep, narrow binding pocket. Due to some experimental limitations, the ligand can be bound only in specific orientation - a ligand edge that is conjugated to an attached large molecule should be headed to the protein surface.

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Rosetta 3 - Applications

SARS-CoV-2: call for compound predictions against protease

Submitted by matteoferla on Sun, 2020-03-22 05:29
Category: 
Small Molecules

There is a recently set up call for compound suggests that may be active against the protease SARS-CoV-2, the etiological agent of COVID-19.

Diamond lightsource XChem team did a fragment screen against it and released last week with many hits, which are starting points for designing the next round of compounds.

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Rosetta 3 - General

Pyrosetta imported after rdkit

Submitted by matteoferla on Sun, 2020-03-01 02:38
Category: 
Small Molecules

I have encountered a curious issue. If I import rdkit before pyrosetta, the latter will not work properly. Rdkit after pyrosetta works fine —so I am basically reporting it here (right place?). Both use Boost wrapping C++ IIRC, so I'm guessing Rdkit changes some setting or imports some library. This code block misbehaves:

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PyRosetta - General

How to freeze ligand during FastRelax?

Submitted by dnamkr on Thu, 2020-01-02 14:53
Category: 
Small Molecules

I want to fix (freeze) ligand during fastrelax because the fastrelax changes ligand conformation weirdly .

This happens even with params file of the ligand.

Therefore, I tried ignore_unrecognized_res, but this option just not outputting the ligand in the result file.

Here I attach screenshots.

 

Thank you

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Rosetta 3 - Applications

GrowLigand

Submitted by allan.ferrari on Sat, 2019-10-19 05:32
Category: 
Small Molecules

Hi all,

Anyone with experience with the GrowLigand mover?

I have as input a holo.pdb structure with a protein target of interest and a small molecule inhibitor which binds with low affinitty (parametrized to be used with genpot). 

I was hopping that this mover would return possible modifications on the ligand so I could rationalize my next steps of synthesis.

Here is my RosettaScripts:

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Rosetta 3 - Applications

Modeling small molecules

Submitted by iGemBoulder on Wed, 2019-09-18 11:53
Category: 
Small Molecules

Hi all,

Just trying to model a small molecule and how it interacts w/ my bigger protein in pyrosetta. 

 

I got this far: 

 

pose2 = Pose()

nonstandard_residue_set = generate_nonstandard_residue_set(pose2, ["ARA2.params"])

pose = pose_from_pdb(nonstandard_residue_set, "combine.pdb")

But pose_from_pdb only takes only 1 argument, how do I get around this? 

 

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