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Small Molecules

Prevention of the negatively charged Nitrogen protonation by coupled_moves

Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear sir and madam,

I have met with the unfavourable addition of 2 Hydrogen atoms onto sulfonamide Nitrogen instead one (NH2 instead of NH) on a ligand during the coupled_moves docking application runs. It is perfomed by the following command:

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When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error

Category: 
Small Molecules

Hi everyone, 

I detected an issue with the small molecule-docking application using rosetta scripts and the setup for doing large-sized libraries screening. In this set up you generally use a "screening_job_file" input that specifies which combination of ligand and protein structures will be used during the simulation. This file looks something like this:

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what factors determine the lowest (best) LigInterfaceEnergy score?

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

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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Ligand docking at specific orientation

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

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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Pyrosetta imported after rdkit

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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How to freeze ligand during FastRelax?

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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