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.

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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 ...
Te-Yo's user avatar
  • 303
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.
Zheng Keong Ng's user avatar
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?
John Deo's user avatar
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 ...
march_happy's user avatar
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 ...
Dembappe's user avatar
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 ...
MH Lee's user avatar
  • 31
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 ...
Oluwaseyi Jaiyeoba's user avatar
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....
littleworth's user avatar
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?) ...
CoryG's user avatar
  • 195
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 ...
albertr's user avatar
  • 71
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 ...
Jim Eric Skogman's user avatar
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 ...
Ahmed M.Osman's user avatar
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 ...
Nurlybek Amangeldiuly's user avatar
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?
Nurlybek Amangeldiuly's user avatar
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: ...
littleworth's user avatar
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
microbeprincess's user avatar
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 ...
abbasly's user avatar
  • 23
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?
Oluwaseyi Jaiyeoba's user avatar
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) ...
ginn's user avatar
  • 31
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 ...
AvadaMouse's user avatar
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 ...
littleworth's user avatar
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 ...
Zac R.'s user avatar
  • 143
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 ...
dnalectronics's user avatar
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 ...
Sherbert184's user avatar
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?
Ahmed M.Osman's user avatar
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 ...
Nurlybek Amangeldiuly's user avatar
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 ...
Linda's user avatar
  • 25
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 ...
Paul Shen's user avatar
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 ...
Zheng Keong Ng's user avatar
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 ...
Andrea's user avatar
  • 113
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 ...
dnalectronics's user avatar
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 ...
sasam's user avatar
  • 11
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'...
littleworth's user avatar
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 ...
neversaint's user avatar
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 ...
djordje's user avatar
  • 125
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 ...
Linda's user avatar
  • 25
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: ...
Evgenii's user avatar
  • 11
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 ...
Khanishka's user avatar
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 ...
ginn's user avatar
  • 31
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 ...
Shafayet Rahat's user avatar
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....
Jatin Kashyap's user avatar
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 ...
apvn's user avatar
  • 11
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 ...
Teabelly's user avatar
  • 111
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 ...
AvadaMouse's user avatar
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 ...
Zheng Keong Ng's user avatar
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 ...
Zheng Keong Ng's user avatar
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 ...
confused's user avatar
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. ...
Shahbaaz's user avatar
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 ...
Shahbaaz's user avatar
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 ...
Rishabh Tripathi's user avatar