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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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 ...
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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 ...
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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
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Unable to install OpenBabel

I am working on building a script that tests the binding affinity of protein-ligand pairs generated by our ML model as positive/negative binding annotations. One of the steps in doing so requires the ...
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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 ...
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Affinity maps and forcefields

I know that before performing docking with AutoDock Vina, we have to compute "vina maps" like below ...
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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 ...
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Generating intercalation site in DNA for custom sequence

Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
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Basic Docking Work Flow

I'm a computer scientist who is now getting into designing new molecules, with the goal that they dock well to a given target. While I'm used to coding up machine learning algorithms in python, I'm ...
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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 ...
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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 ...
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Drug-DNA complex simulation using AMBER

I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will ...
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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 ...
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Does AutoDock Vina require AD4 atom for receptor preparation?

AutoDock tools and MGL tools are specific to AutoDock 4 but we can use them for Vina as well. There are old laid protocol for preparation of ligand and receptor for docking with vina. Gasteiger ...
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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 ...
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How to show that one docking is better than another with Pymol visually

I have the following docking results: Dock_1 has better energy score than Dock_2. What I want to do is to show with Pymol that <...
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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'...
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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 ...
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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....
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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: ...
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How to extract docked ligands from .maegz docking results file sorted by glide gscores in Schrodinger Maestro?

My VLS run completed yielding millions of ligands and I would like to extract top-scored 20000 ligands in a separate file. Incorporating the .maegz output in Maestro is not an option as it fills up ...
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rmsd between re-docked complex and co-crystallized complex

I would like to calculate the rmsd between re-docked complex and co-crystallized complex for docking validation. How do I calculate the rmsd using Pymol? I tried the following command ...
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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 ...
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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 ...
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Building small molecules de novo

Can anyone recommend a protocol for building the 3D structure of a small molecule de novo, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, ...
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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 ...
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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?
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Issues with AutoDock Vina

I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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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 ...
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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. ...
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Error pasing the following line in pdb

I converted an .sdf file containing around 50,000 anti-viral agents to individual .pdb files using OpenBabel. However, when I tried opening the .pdb files with Autodock I kept getting the error below. ...
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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?
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.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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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4 votes
1 answer
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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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2 votes
1 answer
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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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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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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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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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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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2 votes
2 answers
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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 ...
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1 vote
1 answer
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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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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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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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5 votes
3 answers
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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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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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