Questions tagged [docking]
Predicting in silico where a ligand binds within a protein structure or how two proteins bind to each other. Common operations include creating 3D conformers from SMILES, parameterising the ligand, docking itself and scoring.
65
questions
11
votes
1
answer
121
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 ...
6
votes
3
answers
3k
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.
5
votes
1
answer
137
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?
4
votes
1
answer
958
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 ...
3
votes
3
answers
437
views
What is the correct method of identifying the interacting residues for specific molecular docking?
I'm trying to do a specific molecular docking using Autodock Vina in PyRx. So, one way to do that is to mark all of the interacting residues and make sure the grid box encompasses all of that ...
3
votes
2
answers
749
views
Why Do I Get Different Results Each Time From AutoDock Vina?
I just tried to use Vina for calculating binding affinity.
I used the same protein, the same ligand, the same options, but there are different results.
Why do I get different results?
Is it the limit ...
3
votes
2
answers
2k
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 ...
3
votes
1
answer
696
views
Programmatically adding hydrogen and remove water to multiple PDB files
I'm trying to dock a ligand to several hundred PDB files (receptors).
I thus need to prepare the those PDB files like removing water and adding hydrogen.
I can do that manually using Autodock or Pymol....
3
votes
1
answer
135
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?)
...
3
votes
0
answers
53
views
How to select the best ligands in a virtual screening matrix
I have the results of a virtual screening experiment using docking simulations with Autodock Vina. The result is a matrix of 7 (proteins) by 28000 (ligands) with the calculated binding energies for ...
2
votes
1
answer
163
views
Generate ligands candidates based on protein shape
Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
2
votes
2
answers
128
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 ...
2
votes
1
answer
365
views
How to choose docking score cutoff?
I made a virtual screening of a large database (~5M) and want to filter ligand structures for further more accurate screening (from Schrodinger HTVS to SP resolution). My next step is to define a ...
2
votes
1
answer
258
views
Do I need to remove water molecules before protein-ligand docking?
I am going to screen small molecules against a protein target. Do I need to remove all the solvent molecules before performing VLS?
2
votes
1
answer
400
views
How to tell if our ligand-protein docking is good from AutoDock Vina's result
I have perform a ligand-protein docking using Autodock Vina.
The result of the docking looks like this:
...
2
votes
1
answer
45
views
Running into an error when loading Flexaid on PyMol 3.7
I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac.
I was wondering if anyone knows why this isn't running?
Thanks
2
votes
1
answer
3k
views
PDBQT file format
I am trying to understand the source code of the AutoDock Vina, but as I am new to the field of Bioinformatics it is a little hard to understand. It seems like they are using a tree data structure to ...
2
votes
1
answer
1k
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?
2
votes
0
answers
39
views
2D diagram of intermolecular interactions in R
I've docked a large inorganic compound (receptor) with an organic molecule that isn't a protein (ligand). I wanted to see the interaction between them in a 2D diagram, but BIOVIA Discovery Studio (DS) ...
2
votes
0
answers
32
views
How to explain disparities in Flavonoid Docking results between Vina and Schrodinger?
I am planning to dock a protein to Selleck Chem's Flavonoid Library. I have designed two workflows using Autodock Vina and Schrodinger as follows:
Schrodinger
Use their proprietary tools for protein ...
1
vote
1
answer
692
views
How to show electrostatic interactions in Pymol on the wanted residue
I have the following Pymol visual,
The green molecule is receptor and red/yellow is the ligand.
In the ligand I highlighted Lysine (K) residue as yellow.
What I want to do is to highlight and draw ...
1
vote
1
answer
252
views
Extract autodocked protein-ligand connections programatically
I have 2 crystal structures, one for my protein and one for my ligand (I have several protein-ligand pairs). I am using AutoDock Vina to simulate docking, which returns another file of the ligand with ...
1
vote
2
answers
3k
views
Generating PDB file for custom DNA sequence
I asked this question in biology.stack exchange and was referred to this community. I am going to request migration for this question.
https://biology.stackexchange.com/q/105024/67415
I want a PDB ...
1
vote
2
answers
81
views
Do you know any virtual screening libraries with small, soluble compounds?
I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
1
vote
1
answer
284
views
predict the IC50 after using Schrodinger suite Glide tool for docking [closed]
How to predict the half-maximal inhibitory concentration (IC50) of my ligands.
I'm currently using Schrodinger suite software and I don't know how to predict the IC50?
1
vote
1
answer
78
views
Do I need to fill in missing side chains and loops before protein-ligand docking for VLS?
I am going to screen a set of small molecules against a CYP450 2C9 protein target. The structure I am using exactly is 5A5I. Do I need to fill in missing side chains and loops before performing VLS? I ...
1
vote
1
answer
572
views
What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?
I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
1
vote
1
answer
1k
views
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 ...
1
vote
1
answer
92
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 ...
1
vote
1
answer
69
views
How to calculate pharmacophore features?
I asked this question already in the matter modeling forum (here). But i hope this is a better place because the topic is more biological.
I want to use the enzyme ß-Glucuronidase with the pharmit ...
1
vote
1
answer
99
views
building complex drug-dna for AMBER software
I will appreciate if you can please clarify some of my doubts about drug-DNA complex.
I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
1
vote
1
answer
656
views
Python script to simultaneously generate multiple pdbqt files for AutoDockTools?
I have a folder of pdb ligand structures that I'd like to test in some docking experiments with a certain protein using AutoDock Vina.
I am not familiar with Python so I've always been using the ...
1
vote
1
answer
503
views
How to calculate RMSD and binding energy from the already docked ligand-receptor
I have the following PDB file that looks like this.
It is downloadable here. This PDB already contains ligand and receptor together.
The red molecule is the ligand and the yellow is the receptor.
They'...
1
vote
1
answer
52
views
Best way to dock subset of protein PDB and definition of a ligand
I have extracted residue 45 to 88 from a PDB file (2YRQ).
With that I have a new smaller PDB file. Let's call it 45_88.pdb
And I want to dock it to some other full protein.
My question is what's the ...
1
vote
1
answer
251
views
Visualizing protein-ligand interactions with LIGPLOT or any other suitable software?
I have used DOCK software to dock 10 ligands into the protein structure.
I want to generate a pdb file that contains all 10 binding modes of the ligands together with the protein. So all together in ...
1
vote
1
answer
43
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 ...
1
vote
0
answers
80
views
Renumbering atoms in PDB using OpenBabel
I'm trying to add polar hydrogens to protein (PDB ID 3l3l cleaned from water and ligands) and convert it to PDBQT using OpenBabel by:
...
1
vote
0
answers
225
views
Errors in AutoDock
I am using Autodock and I'm getting an error in the step where we get the glg file (i.e. Run--> Autogrid) I am not sure what should I do...Please help me if someone knows how to tackle this. Plus ...
1
vote
0
answers
43
views
Is there any way to handle CONECT records in AutoDock Vina?
I modelled a macromolecule/receptor using Avogadro and exported it as receptor.pdb. Many entries in this file are CONECT records. If I try to run AutoDock Vina with it, this happens:
So, if I prepare ...
1
vote
0
answers
10
views
Define and calculate pep_sc and pep_sc_noref in pyrosetta
I can calculate total rosetta energy score of a peptide-protein complex. However, when using flexpepdock module from pyrosetta I didn't find anything direct parameter like pep_sc or pep_sc_noref in ...
1
vote
0
answers
168
views
Creating maps.fld file of protein for AutoDock GPU
I want to use AutoDock GPU, which accepts protein.maps.fld and ligand.pdbqt files.
Since I am performing high throughput virtual screening, shall I just load protein AutoDockTools and create protein....
1
vote
0
answers
36
views
Good molecular docking software?
I'm looking for some good molecular docking software (preferably, one that comes with a Python API). I obviously found Vina and that's been quite helpful but I was wondering if there's anything out ...
1
vote
0
answers
46
views
Understanding protein-peptide docking analysis
I want to explore some potential reactive peptides and seems a common step to conduct some form of docking analysis. I have a question about the theory and a practical question.
Practical question:
An ...
1
vote
0
answers
87
views
Ligand and protein preparation in Vina docking
I am an undergraduate novice, from CS major, intending to run a virtual-screening run using Autodock Vina. A few questions in this regard:
How to choose the best charge model for the ligand?
By ...
1
vote
1
answer
90
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 ...
1
vote
0
answers
72
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 ...
1
vote
0
answers
73
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 ...
0
votes
1
answer
51
views
Generating 3D coordinates error
I have been trying to convert a multi entry sdf file to pdb using openbabel. Everytime I check the Generate 3D coordinates box I end up with .ENT files instead of .PDB files. What am I doing wrong.
...
0
votes
2
answers
2k
views
.SDF file to .PDB file
I am currently working on identifying effective antiviral compounds against the corona virus. I have downloaded the Covid-19 AntiViral Candidate Compounds Dataset from the www.cas.org webpage, the ...
0
votes
1
answer
99
views
Energy minimization of molecules
I have 3000 molecules which I need for docking but before that I need to perform energy minimization for all the molecules and it is taking a long time because I am doing it one by one. So is there a ...