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protein-ligand docking rescoring with interfaceAnalyzer

Submitted by syntekabio2019 on Sat, 2020-12-19 03:59
Category: 
Docking

 Hi 

 My name is Jong hui Hong

 I'd like to rescore docking result structure made by Rosetta-script application with InterfaceAnalyzer

 But InterfaceAnalyzer application binary couldn't be found in binary folder ( rosetta-source/main/source/bin) .

 Is there any other folder for that application ?

 It seems that InterfaceAnalyzer source is there in Rosetta source

 Can there be something wrong with my rosetta installation?

 Any kind of suggestion or answer would be appreciated 

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Rosetta 3 - Applications

Docking high and low resolution

Submitted by nasim.soltani58 on Thu, 2020-12-17 10:26
Category: 
Docking

Hello,

 

I need to know about the method that is used for both high and low resolution docking. I know it is markov chain monte carlo, but I need to know in more details. Could you please provide me with a paper or any other resources about the method used for docking (in details)?

 

Thank you very much

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PyRosetta - Applications

Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?

Submitted by Corvin on Wed, 2020-12-16 04:58
Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Sir and Madam,

I have performed a lot of attempts in order to conduct the coupled_moves docking with ligand without it protonation. I need to specify that this ligand (in his physiologically active form) has only one Hydrogen on his sulfonamide site. Nevertheless, despite the absence of any other Hydrogens both in input .params, MOL2 and PDB file, a lot of sites (sulfonamide Nitrogen with additional undesirable Hydrogen, as well as some Carbons on a benzene ring and tail) get protonated.
By the way, Ligand_Dock application also protonates all possible ligand sites.

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Rosetta 3 - Applications

Assesing the docking

Submitted by nasim.soltani58 on Sat, 2020-12-05 21:19
Category: 
Docking

Hello,

I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:

Name of Chain_1: predicted.pdb
Name of Chain_2: true.pdb
Length of Chain_1:  289 residues
Length of Chain_2:  579 residues

 

TM-score= 1.00000 (if normalized by length of Chain_1)
TM-score= 0.49914 (if normalized by length of Chain_2)

 

 

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PyRosetta - General

Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms

Submitted by Corvin on Wed, 2020-12-02 04:00
Category: 
Docking
Small Molecules
Chemically Modified Residues

Dear Rosetta people,

I am trying to dock ligand, which possesses by sulfonamide NH group to the target protein with a help of coupled_moves application by the following command:

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Rosetta 3 - Applications

Constraints residues in different chain in protein-protein docking

Submitted by nasim.soltani58 on Sat, 2020-11-28 10:24
Category: 
Docking

Hello,

 

I want to dock two proteins. I have some constraints between residues of different chain (here chain A and B).

For eaxmple:

For residues number 15 of chain A, and residue number 271 of chain B, I have the following information:

The minimum distance between residues is 0, and the maximum distance is 6.

 

How can I add constrain for something like this case (I mean when residues are in different chain)? How can I specify that residues are in diffrent chain?

 

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PyRosetta - Applications

polymer docking using rosetta scripts

Submitted by syntekabio2019 on Fri, 2020-11-27 01:51
Category: 
Docking

 

   Hi  My name is  Jong hui Hong

   I'm trying to dock the ligand which has 5 chemical linked via covalent bond( ACE-UB4-DPP-GLY-GVE) using Rosetta-Scripts

   I changed ligand residue name into PRD and made conformer using obabel , made paramter file using molfile_to_params.py without any problem

   but when I run docking using  rosetta_scripts.linuxgccrelease

  I got the following error

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Rosetta 3 - Applications

Extending Pyrosetta toturials for docking by adding constraints

Submitted by nasim.soltani58 on Thu, 2020-11-26 13:16
Category: 
Docking

Hello,

I followed pyrosetta tutorials for docking.  I did something like the following: 

scorefxn_low = create_score_function("interchain_cen")
jd = PyJobDistributor("output", 100, scorefxn_low)
while not jd.job_complete:
    cen_pose.assign(starting_cen_pose)
    dock_lowres.apply(cen_pose)
    jd.output_decoy(cen_pose)

 Then, I selected the candiddate with lowest score.

 

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