Docking

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ligand dock into HEM containg pdb

Submitted by syntekabio2019 on Thu, 2022-01-20 03:05

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Docking

Hi all

I would like to dock unknown chemical into PDB which have HEM as a cofactor

But I want to fix the HEM molecule fixed during docking with constraint statement below

                 <RESIDUE_SELECTORS>
                        <ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
                </RESIDUE_SELECTORS>
.

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charge grid in rosetta ligand docking using rosetta script

Submitted by syntekabio2019 on Mon, 2022-01-17 23:53

Category:

Docking

Ho all

Recently I'm trying to do protein-ligand docking with rosetta scripting interface

what I want to do is to incorporate charge grid in rosetta script xml file as shown below

                 <SCORINGGRIDS ligand_chain="X" width="25" name="charge">
                        <ChargeGrid grid_name="charge" weight="1.0"/>
                </SCORINGGRIDS>
.

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any examples of calling SnugDock from pyrosetta?

Submitted by antonkulaga on Thu, 2021-12-23 16:13

Category:

Docking

I am writing a python script that will do docking for my antibody-antigen samples, however, I could not find any SnugDock code examples with pyrosetta. Could you please give at least one?

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PyRosetta - General

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SnugDock or RosettaDock for HDX-MS data

Submitted by hanzhiz on Thu, 2021-12-16 09:18

Category:

Docking

Hello,

A general question would be whether there is a docking protocol for HDX-MS. Can I get a share?

Then I have two questions to the paper "Robustification of RosettaAntibody and Rosetta SnugDock" from Gray's group:

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Global ligand docking with Rosetta script and PyRosetta

Submitted by tisozaki on Tue, 2021-12-14 17:16

Category:

Docking

Hi all,

Is it possible to perform global ligand docking with Rosetta script not PyRosetta?

I found the tutorial for global ligand docking in PyRosetta. ( https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb )

But, I could not find any explicit example for global ligand docking with only Rosetta script.

Thank you,

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Rosettasurface in Pyrosetta 4

Submitted by Oaham on Mon, 2021-11-22 23:35

Category:

Docking

Greetings,

I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.

Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4?

Thanks very much!

Hao

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Multi-metric enzyme docking with substrate

Submitted by Wang Zhe on Sat, 2021-11-20 04:41

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Docking

Hello,

I want to get a series of enzyme-substrate binding pose in one step of my research, but I met some questions:

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ligand docking

Submitted by hong wei on Thu, 2021-11-18 05:01

Category:

Docking

Hello:

I've been trying to run the ligand docking, I want to ask hoe to specify the docking regin?

Thank you

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Problems with waters in CoupledMoves application

Submitted by Corvin on Tue, 2021-11-16 07:16

Category:

Structure prediction

Docking

Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

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