Questions tagged [docking]

questions concerning docking - a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.

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10
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1answer
160 views

Are there good tutorials that explain how to use experimental data to customise the force field in AMDock Vina?

I am not a chemist, but I know how to use AMDock to predict the binding affinity of a small molecule to a protein. There is a particular target for which AMDock Vina, with its default force fields, ...
6
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0answers
34 views

Construction of dimeric protein models, selection and refinement [closed]

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...
4
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1answer
33 views

Ligand-protein molecular docking with different protonation states

It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational ...
10
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4answers
131 views

Protein structure prediction

I want to perform a molecular docking between several ligands and the transmembrane domain of a protein. For this protein I only have the amino acid sequence, so it's necessary to do two things: ...
5
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1answer
26 views

How to interpret the affinity in a protein docking - ligand

I'm performing a molecular docking using a trans-membrane protein and several ligands. For the first ligand, the best conformation gave a binding energy of 110 kcal/mole, being 50 kcal/mole the ...
8
votes
1answer
109 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
4
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1answer
23 views

Procedure to validate glide docking without a reference ligand on Autodock vina

How can I perform a score-in-place procedure with autodock to validate ma glide docking? It is a new software for me and I don't Know how to use it and how to proceed. Thanks in advance for help.
5
votes
1answer
57 views

Docking validation RMSD over 3, How can I fix it?

I performed a molecular docking and when I tried to validate it, the RMSD values are over $3 \overset{\circ}{\mathrm{A}}$. I don't understand how I can fix it. Could someone help me? Thanks in advance....
6
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1answer
96 views

How can I validate docking result without a co-crystallized ligand?

I have to validate one of my docking protocol but I haven't a co-crystalized ligand. There is a way to validate it? Thanks in advance.
4
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1answer
40 views

How to compare structural results by superposition and compute RMSD to validate docking?

I wonder how to use this panel to validate docking? I tried and the results are a disaster: Thanks in advance.
10
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1answer
143 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
5
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1answer
153 views

How to calculate RMSD with GLIDE?

I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
9
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1answer
68 views

Docking proteins with glycans

Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
14
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8answers
2k views

What are some free programs to do docking?

I'm interested in doing molecular docking. What are some free programs for it and what are their pros and cons?
7
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1answer
56 views

Which non-commercial software can be used to dock two proteins?

I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below. Since there are many docking ...
10
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2answers
244 views

What are the factors to consider before docking 2 proteins?

With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
5
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1answer
88 views

Why am I losing bonds when I use PACKMOL on two proteins?

I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code: ...
8
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2answers
120 views

Docked pose and energy minimization

Is it useful to energy minimize a docked pose before scoring it? I am speaking in the context of protein-ligand systems. Does the energy obtained after minimization correlate better with experimental ...
10
votes
1answer
132 views

MM-GBSA from Induced Fit Docking on Maestro

How can an MM-GBSA(molecular mechanics energies combined with generalized Born and surface area continuum solvation) calculation be done from an induced fit docking (IFD) output? I performed an IFD ...
10
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3answers
227 views

How I can analyze and present docking results?

I did a docking job and got a score of -5.69 kcal/mol and a value for MM-GBSA of -60 kcal/mol. I should analyze these results for my thesis but do not know how to comment on them. Does anyone have ...