Questions tagged [docking]

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Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?

Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations. Specifically helping screen existing drugs against ...
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How to rescore docked protein-ligand poses?

I have a set of several protein-ligand complexes in pdb format which I generated using Schrodinger software. I would like to rescore the whole set to obtain scoring results once again, given that I ...
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1answer
56 views

How could I match atom orders between a .mol2 and a .pdb?

When I was drawing conformation of Autodock result, I noticed that Autodock generated pdbqt from dlg has some structural problem (e.g. Benzene ring missing), and wants to correct this. However I ...
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1answer
32 views

What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?

What score value is considered acceptable when using Vina Autodock tool for molecular docking simulations?
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1answer
24 views

Are crystal structure of Ligands used in volunteer computational docking like FightAIDS@home?

In large Volunteer computing for molecular docking projects such as FightAIDS@home, do they use the original crystal structure of ligands in docking or unconfirmed structures of ligand?
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1answer
29 views

Which of these enzymes is a better target for virtual screening?

I am a MSc student in Applied Biochemistry. For my Masters Thesis, I will be doing some research about finding new potent inhibitors for a specific enzyme of my choice using molecular docking (virtual ...
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1answer
23 views

AutoDock 4 -soft docking

How could I turn on/off the smooth potential in AutoDock4? I need to do two docking. The first one is soft docking with smooth potential and the second is re-docking without the smooth potential.
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2answers
76 views

Asking for Docking programme

I'm tring to do my M.Sc. research and I Have to do Docking to save some money as I cannot try all the compound that I'm working on. what is the best Protein-Ligand Docking programme? And anyone has ...
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2answers
230 views

What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?

I need to lightly verify a set of docking simulations from the reference RMSD of the outputs, and as we all know reference RMSD depends on the initial coordinates of the ligand set. What value of ...
1
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1answer
17 views

Purpose of correlating docking score with catalytic efficiency(Kcat/km)

What is the purpose of correlating docking score with catalytic efficiency (kcat/km)? I saw some papers are doing this, is it to validate the docking protocol? Lets say the docking protocol is ...
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1answer
39 views

Post docking evaluation

What to do after protein-ligand docking? Is there any necessary or enhancement step recommended after docking to validate the confirmation of highest score is the best? For your information, I am ...
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0answers
19 views

How to find Wild Type (WT) protein structure on Protein Data Bank (PDB)?

Currently, I am working on Galactose oxidase enzyme for protein docking and I am totally new to it. I have to study how mutation on specific residue will make mutated galactose oxidase better than the ...
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3answers
117 views

Why is it necessary to add hydrogen and delete water before protein-ligand docking?

What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
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16 views

Rescoring For Docking Poses

I want to do Consensus scoring of my docking poses, could any one help me which are the good free available rescoring programs. I have used Autodock vina, MOE, AMBER, but i want to know about some ...
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35 views

NPDock - service unavailable [closed]

NPDock service http://genesilico.pl/NPDock/ is unavailable, at least that's the message that shows after you try to submit a job. It's been like this for the last few weeks. Contact email address ...
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1answer
83 views

What algorithms exist for reverse protein folding?

Are there any algorithms already in existence for reverse protein folding/docking (e.g. taking a desired surface map/docking profile and generating DNA which will produce a protein to fold into it?) ...
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1answer
68 views

How can I dock a protein to a nucleic acid?

I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules. What tool can I use?
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1answer
99 views

What are the optimal parameters for docking a large ligand using Hex?

I'm looking to dock a large ligand (~90kDa) to a receptor slightly larger receptor (~125kDa) using Hex. If anyone is familiar with docking large structures, are there any recommended parameters for ...