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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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1 answer
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Blind docking and targeted docking

I used Autodock Vina and UCSF Chimera to perform blind and targeted docking on a protein from the RCSB database and a molecule I had optimized with Gaussian software.The results are as follows: The ...
sarra6's user avatar
  • 579
2 votes
1 answer
36 views

How to calculate pharmacore features?

Cross-posted at Bioinformatics.SE. I want to use the enzyme ß-Glucuronidase with the pharmit database. I uploaded my file for the receptor from pdb file. How can I get the pharmacore features? So one ...
Andrea's user avatar
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1 vote
1 answer
25 views

problem with the input at ZINCPharmer

I need to search for possible inhibitors for an enzyme. So I found the website ZINCPharmer and a publication which seems to help me out with my problem. When I enter the website I cannot submit any ...
Andrea's user avatar
  • 856
3 votes
0 answers
47 views

Running molecular docking simulation between two proteins

i did run docking simulation between two proteins on HADDOCK server but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it best ...
Imane Yamari's user avatar
1 vote
1 answer
31 views

Complex formation site between polymer and external compound

I am studying about conjugated polymers in sensors applications. I want to conduct structural of complex and its properties (such as HOMO-LUMO etc.). Is there any software for docking that external ...
Duy-Minh Hoang's user avatar
4 votes
0 answers
90 views

Are there any open-source or free softwares for covalent docking of multiple ligands?

I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of ...
biryaniboi's user avatar
2 votes
0 answers
47 views

How to add Samarium atom type in Autodock Vina? [closed]

While trying to perform docking of a protein containing Samarium atom using Autodock-vina in Ubuntu, the following error arises. "ATOM syntax incorrect: "Sm" is not a valid AutoDock ...
Madhusmita's user avatar
3 votes
0 answers
419 views

How to add atom types in Autodock Vina [closed]

The following problem arises when I use Vina for virtual screening. Vina seems to have only one calculation program, so how do I add the required atomic force field parameters? "ATOM syntax ...
user19894668's user avatar
2 votes
0 answers
37 views

Literature applying molecular docking into MD-simulated structures of proteins

This is quite surprising, at least for me, that many papers performed molecular docking of an unsimulated (original) protein structure and MD simulation of a protein in a timescale to check the ...
làntèrn's user avatar
  • 231
2 votes
0 answers
656 views

Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files [closed]

Cross-posted on Chemistry.SE. I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
user3765252's user avatar
5 votes
3 answers
134 views

Is generating conformers necessary for molecular docking studies?

I have seen some research papers on molecular docking studies using some conformer-generating softwares like CORINA, OMEGA, etc. and they used these softwares to generate conformers of a molecule and ...
làntèrn's user avatar
  • 231
1 vote
1 answer
221 views

Exporting IFD output to poseviewer file

I have an output from induced fit docking (IFD) in Maestro. I want to calculate the MM-GBSA for the output obtained from IFD in Maestro (Schrodinger) for which poseviewer file (.pv.maegz) is required. ...
Abhinav Srivastava's user avatar
5 votes
0 answers
440 views

Autodock Vina Error on Chimera: Service "local" unavailable [closed]

I was confronted with an error, upon trying to dock a minimized ligand to a target protein, that the "service 'local' [is] unavailable". I then realized ...
Mas's user avatar
  • 211
5 votes
1 answer
584 views

Why are ligands restrained when simulating a protein-ligand complex with MD?

Currently I'm doing an MD simulation of a protein-ligand complex using GROMACS. In the tutorial it mentioned the process of Restraining the Ligand. Why do we do it? Is it absolutely necessary?
littleworth's user avatar
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5 votes
2 answers
2k views

How can I get Vina to recognise boron atoms?

I am trying to dock a ligand that features a boron (B) atom. AutoDock Vina throws an error with the following message: ATOM syntax incorrect: "B" is not a valid AutoDock type. Note that ...
Shredderroy's user avatar
6 votes
2 answers
1k views

How to initiate protein-ligand docking with MD simulation tools

I have two PDB files (each corresponding to a ligand and a receptor). Each downloaded separately from PDB. I'd like to perform ligand to protein docking process with MD with GROMACS or Amber. Using ...
littleworth's user avatar
  • 1,674
10 votes
1 answer
240 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, ...
Shredderroy's user avatar
6 votes
0 answers
41 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 ...
SharkCaller's user avatar
4 votes
1 answer
526 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 ...
SharkCaller's user avatar
10 votes
4 answers
314 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: ...
SharkCaller's user avatar
5 votes
1 answer
3k 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 ...
RoyBatty's user avatar
  • 367
8 votes
1 answer
491 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, ...
RoyBatty's user avatar
  • 367
4 votes
1 answer
155 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.
Giu's user avatar
  • 477
5 votes
1 answer
441 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....
Giu's user avatar
  • 477
6 votes
2 answers
770 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.
Giu's user avatar
  • 477
4 votes
1 answer
206 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.
Giu's user avatar
  • 477
10 votes
1 answer
167 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 ...
Paulie Bao's user avatar
  • 3,973
5 votes
1 answer
1k 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 ...
Giu's user avatar
  • 477
9 votes
1 answer
178 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 ...
Ivan's user avatar
  • 879
16 votes
8 answers
4k 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?
Roselyn Lemus-Martin's user avatar
7 votes
1 answer
77 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 ...
SaiSmaran S B PES1201701189PES's user avatar
11 votes
2 answers
286 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 ...
SaiSmaran S B PES1201701189PES's user avatar
6 votes
1 answer
292 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: ...
SaiSmaran S B PES1201701189PES's user avatar
8 votes
2 answers
361 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 ...
BND's user avatar
  • 1,341
10 votes
1 answer
595 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 ...
Giu's user avatar
  • 477
12 votes
3 answers
5k 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 ...
Giu's user avatar
  • 477