Molecular Docking - Science method

I used AlphaFold to predict the 3D structure of a protein target that is not available in PDB. However, the prediction has low confidence values (low pLDDT scores). Should I proceed with molecular docking using this structure, or should I refine it first? If refinement is necessary, what are the best approaches to improve its reliability for drug design? Any recommendations or relevant research papers would be greatly appreciated!

I am having problem in the selection of monomeric human insulin pdb structure for the development of aptamer via molecular docking and molecular dynamics. How should I select the best suit one which represent the native structure of active insulin in human body. Which technique is preferred, is it X-ray diffraction or NMR structure? Based on the validation report, I found out that there are outliers in all the pdb structure, how should I fixed it. Before molecular analysis, the pdb structure should be properly checked and repaired, is there any detailed guidelines/protocol on this? I have no idea on how to identify the errors (things to be investigated) and the way to fix it. Your opinion is highly appreciated, thank you.

Excuse me, I am learning how to do molecular docking and some targets I have docked have resulted with many favorable bonds but also with many unfavorable bonds in red. My question is, is there any criterion to know if the simulation, despite the unfavorable bonds, could allow molecular docking and induce or inhibit some biological mechanism? Thank you very much for your help.

Is it common practice to do multiple trials of your molecular docking simulation? For example, you want to check binding affinity of a certain phytochemicals with an enzyme. Do you have to perform the same molecular docking algorithm thrice (for three trials) or is just once enough? This is using Autodock Vina.

this is need for molecular docking

Hello, do you need basic programs for molecular docking?

Dear colleagues,

I have conducted an experimental study on NO production using RAW 264.7 cells and obtained promising results. I am now looking to deepen my understanding of the underlying mechanisms through in silico approaches, such as molecular docking, pathway analysis, or ADME/Tox predictions.If you have expertise in in silico methods or are interested in collaborating on this project, please feel free to contact me. I would greatly appreciate your insights and guidance to advance this work.Thank you in advance for your time and consideration!

Best regards,

Hi researchers,

I have downloaded 20,000 compounds from databases in .sdf format in a single file (size: 108 GB).

Could someone guide me on splitting the enormous single ligand file into separate files? In the past, I've used open babel to convert the file from .sdf into .pdb. But, I wish to split this vast database ligand file into separate ligand files for molecular docking. Can I use the Open babel, command prompt for this work? Kindly do give suggestions on this issue.

thanks in advance

this technique is very important to research can any one help me for my research

Hi

Can anyone suggest free and easy-handling AI-assisted software or web servers for protein-ligand molecular docking and molecular dynamics? f

I am using HDOCK to perform molecular docking, but HDOCK has a limit of 500 nucleotides for the receptor. However, we want to perform docking on the entire 3' UTR region. Can anyone suggest a solution to this problem?

I downloaded the ligand file in SDF format from the ZINC database, then converted it into PDB format using OpenBabelGUI. This file was then opened in AutoDock Vina and converted into PDBQT format, and finally, it was docked with the enzyme's active site. After docking in the command prompt and splitting via vina_split.exe, different poses of the ligand in the enzyme's active site were found. When this ligand file is opened in Biovia Discovery Studio for visualizing ligand interactions, I face difficulties with the ligand breaking apart. If anyone can help me resolve this problem, I would be grateful.

Dear all,

I am working with five proteins and would like to investigate their interactions when present together in a single solution. Could you suggest any online tools or platforms capable of performing molecular docking for multiple proteins simultaneously?

Thank you for your assistance.

Best regards,

I was doing blink docking using AutoDock Vina. All the parameters are same, ligand and receptor also the same, just that the grid box center is a little bit different (I did at different time frame, so I set the grid box twice with autodock tools). By principle, isnt it both the results should be the same, since the grid box have covered the whole receptor. Can any one explain why I get different results? And which one should I take?

Please suggest me how to select a protein in U-87 cell line for molecular docking study of isatin derivatives against cancer cell.

What is the criteria to select a suitable protein for docking study?

I want to check the antioxidant activity of a organic derivative on xanthine oxidase enzyme using molecular docking . For this I have downloaded the Bovine milk XO enzyme from PDB. The active site of the enzyme contains molybdopterin cofactor. Autodock4 shows some errors when I try to run it. I think this may be due to the Mo atom. Anyone please help me to resolve this problem.

This is what it shows on my computer.

Please help

I have predicted (human) resistin structure using modeller, phyre and itasser and none of the structures I received showed suitable binding energy with known drug (eg-masoprocol) after docking, and I am unable to complete the study.

Hi guys, I am trying to design an aptamer for insulin via in silico methods.

I used aptcad webserver for docking but kept showing failed, stated to try again with smaller molecule. Is it because the insulin structure too big? But my target is insulin, how should I do in this case?

Anyone can help with this situation?

The screenshot of the error has been added. It popped up while the receptor molecule was adding just in the beginning of the process.

After greetings...

Can I get the full molecular docking program...

I downloaded the 2015 version but it doesn't work...

I hope anyone with a full and activated version can help me...

Thank you very much

I am not a specialist in molecular docking, but the applications interest me. I would like to know if it is possible and interesting to perform molecular docking of a mixture of molecules on the same target? And is there a computational technique to predict the assembly of molecules in the most stable state before starting the docking?

Thanks

It’s always exciting to see how computational tools are revolutionizing drug design and discovery. Techniques like molecular docking, pharmacophore modeling, ADME Study and DFT simulations are not only speeding up the process but also allowing for more precise predictions of molecular behavior. These advancements enable us to dive deep into molecular interactions and predict therapeutic potential with greater accuracy. It’s fascinating to witness the fusion of chemistry, biology, and technology in the development of innovative solutions for real-world challenges.

Hi all, I am working on the protein-protein interaction study. The homology modeling protein structure was in good quality which Ramachandran plot shown more than 97% of aa are in the most favoured region. In addition, the sequence similarity is high which is about 70% similarity to the reference crystal structure. Hence, I proceed to protein-protein docking, which docked the homology protein structure (receptor) with another protein crystal structure (ligand). I have generated a set of molecular interaction data and is going to publish the works. However, I found that most of the journal will require MD. Is there any journal that can accept the molecular docking data without MD?

Could you please advise on how to perform molecular docking for polysaccharides (large molecules)? I have previously used Glide in Schrödinger for small molecule docking, but what would be the most appropriate software or approach for handling polysaccharides?

Could you provide any further guidance or recommendations on this matter?

Hello everyone,

I am currently working on a molecular docking project and have obtained results that I need help interpreting. I would greatly appreciate any guidance on how to analyze these results effectively, including insights about RMSD (Root Mean Square Deviation), binding affinities, binding poses, hydrogen bonds, and the amino acids involved in these interactions.

Any resources, tips, or personal experiences you could share would be immensely helpful!

Thank you in advance for your assistance!

Being a newbie, i want to eqip myself with the necessary Bioinformatic tools including molecular docking...Important materials, videos to introduce me to these tools are welcome..I really have a knack in this field.

I have tried many times to dock ubenimex n (Compound CID: 72172) with a protein but every time the ligand breaks into two pieces. Kindly help. i have used chemdraw, 3d sdf file, gaussian fchk file, mol2 file to convert the ligand into pdb file but every time Autodock splits the ligand. Hydrogens and charges were added. ligand is neutral.

Can multiple instances of the same ligand be docked to one macromolecule? For instance, can one ligand be docked and then the output used as input for a second docking of the same ligand, and so on?

I want to use ReverseDock for off-target analysis in molecular docking. How authenticate and reliable are the results of ReverseDock and can I put those results in my research paper ?

Hi every one

I have a peptide library (around 300 peptides) that I would like to dock peptides to its target while I want a high throughput molecular docking webserver or software to do this. Does anyone know any web server or software for this purpose?

Hi

I would like to do molecular docking for my protein with metalloids such as arsenate, nitrate, selenate. I am able to dock for nitrate and selenate on the CB dock website. However, I am getting errors when I try to do that for arsenate. Is there a way to find why the error message and how to fix it in CB dock? or please suggest good and reliable free software for docking in Mac OS? I have the latest version of OS software (Monterey).

Please suggest or recommend, how to perform this work.

Thanks in advance

Hi everyone, I'm currently working on an autodock4 and I've received those warning in my running process. I don't know how to fix or how it affects to my final results. Attached below are my dpf file and cmd warning.

Thanks for your advices.

I use the free version of PyRx. It is bugging me for quite some time that every time I try to dock a specific ligand with a specific protein, the binding affinity differs. Sometimes, the difference is too much. For your convenience, I am giving an overall idea of how I do that.

1) At first, I prepare the ligand and protein and minimize their energies with different softwares.

2) Then I dock them in PyRx.

I follow the the procedure every time. However, the results are not the same. Can anyone help me out?

what are informations that we extract from DLG file of autodock4 and what conclusion can we get

I have performed multiple ligand molecular docking using AutoDock Vina in windows. There is any way to extract lowest binding energy value from all log files rather than copying value by opening each file one by one?

I am beginner in molecular docking field. I have read a lot research papers and books but I wanted a suggestion about any material that could help me clarify ideas about the biophysical basis of molecular docking.

Many thanks.

i would like to learn drug design specially docking but i dont know how to start since i have no previous experience in this field as being a polymer chemist

Good evening Ma/Sir, trust you all are in good health. I am interested in learning docking using Autodock and UCSF chimera. Please where can I get materials (videos) that can guide me especially in the area of active/binding site determination. Thank you.

Kind Regards

I am trying to see whether there is an interaction between a specific virus protein and a natural compound (which will serve as my ligand), however I have no experience in molecular docking. I am aware that there are certain steps that need to be undertaken for me to get my protein and ligand both ready before I run molecular docking, but I am not sure where to start or how.

Some guidance would be very much appreciated. Thank you in advance.

Hello everyone,

How can I prepare a hydrophobic ligand for molecular docking? Is there any tool for hydrophobic ligands?

Which tools are best for prediction of binding pocket or active site of protein to perform molecular docking?

Thanks!!

What are off-targets and how to perform off-target analysis in molecular docking ?

How can we select the best ligands among more than 60K compounds for a protein based on their binding affinities?

These compounds are from an antiviral library and I performed molecular docking using autodock vina.

Should I select by ranking them on the basis of high to low binding affinity and then taking the top 10 or 100 ligands from it?

Collaboration possible

I am trying to dock a small ligand into a protein containing three Mg2+ ions that are essential for ligand binding using AutoDock Vina. However, when I prepared the receptor pdbqt file via the Autodock tool, the charge of Mg2+ was zero. Can you guide me on how to address this problem? Thank you so much.

I have done molecular docking for 70 pdb comprises 30 pdb with ligand and 40 pdb without ligand against 418 ligand compounds from Drugbank. So, for each pdb, there are 70 different results for each 70 pdb. So, how can I visualize the interaction for each pdb against 418 ligands automatically by using Biovia Discovery Studio without manual method? The criteria that I am looking for are the position of ligand inside the binding site and the 2D diagram interaction.

I am attempting to convert several .sdf ligands (2D) into .pdbqt files using the Open Babel program for molecular docking. I have followed the steps below:

After completing these steps, I encountered a fragmented structure, as shown in the picture. What could be the reason for this output, and how can I rectify it? Please provide your suggestions. Thank you.

Comandline I used:

obabel -isdf *.sdf -h -osdf -O*.sdf --gen3d

obminimize -ff MMFF94 -sd -n 10000 *.sdf

obabel *.sdf -omol2 -m

obabel *.mol2 -opdbqt -m

I have not used script based method yet I have seen some people have the same problem with script as well.

Note: This problem is coming with 2D.sdf files not with the 3D.sdf files.

Hello,

I was wondering if there is a procedure available for implementing and running an exhaustiveness setting of 24 in Autodock 4.

My goal is to conduct a comparative analysis between the pose results obtained from Autodock Vina and Autodock 4 while maintaining consistent control parameters, including exhaustiveness, for both programs. Is running exhaustiveness = 24 possible in Autodock 4 just like in Vina? If so, how does one go about it?

Thank you in advance!

Hi RG colleagues,

Wondering if there are any researchers with expertise in molecular docking who would be interested in a small collaborative project? I am interested in predicting if a small selection of natural products are active against specific nociceptive receptors (such as TRPV1), and investigating the features responsible for their activity. I am hoping that we could get a publication out of the project.

Kind regards,

Joel

I am Sai Pavithra doing research in Biotechnology related to herbal medicine. I did molecular docking using Autodoc Vina software. I am preparing for my viva voce. Kindly can anyone please tell me how should I present my molecular docking data for viva.

Dear All,

I downloaded ZINC000000001115 (Leukeran) in SDF 3D structure from Pubchem, https://pubchem.ncbi.nlm.nih.gov/compound/2708#section=3D-Conformer (figure 1).

Then I converted the ZINC000000001115.sdf into bdbqt files, with the use of Openbabel and AutodockTools, then I got the ZINC000000001115.pdbqt and checked its structure with Discovery Studio 2020 (figure 2). However, ZINC000000001115.pdbqt looks like a broken structure. Is the ZINC000000001115.pdbqt file good for further molecular docking or there is a problem during conversion?

Looking forward to your opinions and solutions.

Thank you and best wishes,

Xiaohua

Dear scientists, I need help with molecular docking with Autodock.

- When I upload the Protein or Ligand structure, the command "swig/python detected a memory leak of type 'BHtree *', no destructor found" appears on the screen (Picture 1).

- Then, I can't Run AutoGrid or AutoDock. When I press the Launch command (with files created), it only results in a window like this and sometimes nothing happens and The error log says "Sorry, I can't find or open Grid Parameter File "C:/Users/..." . I have everything in one folder already so it should find the files (Picture 2).

Can anyone tell me what have I done wrong and how to correct it? I tried a few times and it is still the same.

I look forward to receiving help from you.

Thanks very much.

Dear Docker community,

I'm a beginner at using molecular docking, and I'm facing a problem when I want to open or drop a pdb file on Autodock tools. The folder is saved with the extension.pdb; however, it cannot be run on ADT because it generates an error message.

I don't know how I can deal with such a problem; I need your urgent help.

Molecular docking software/ websites?

HI All,

I'm performing energy minimization for all 31,000 ligands from the CMNP Database. The file I downloaded is a single SDF containing all the structures. I'm using the OpenBabel module in PyRx for the energy minimization, but the program keeps getting stuck and exits automatically before completing the task. When I try to rerun it, the process starts from the beginning and gets stuck again. Could you suggest a solution to this problem, or recommend an alternative method to complete the energy minimization?

I want to do energy minimization for all the ligand and save each as PDBQT.

I have attached a screenshot of the error I'm getting from PyRx.

Thank you

What softwares can I use and how do I start it?

Molecular docking Software or online application compatible with Mac OS Sonoma 14. Thank you!

After performing the molecular docking of ligands containing chlorine atoms, the .pdb files of the complex of the conformers of interest and the respective receptor were generated from the .dlg.pdb output file using the Maestro program. When trying to visualize ligand-receptor interactions, Discovery Studio shows alkyl-type interactions with the chlorine atom.

Does anyone know how this error can be fixed?

I've done molecular docking experiments with both AutoDock Vina and AutoDock. Now I'm interested in running molecular dynamics (MD) simulations to investigate the interactions between the docked ligands and their target proteins. Could you kindly suggest a suitable software for this task?

Good afternoon!

I am new to molecular docking. I have watched lessons on youtube, read forums, but still have questions about the algorithm of the work. I hope to find answers here. Sequence of work in AutoDock4: 1. protein preparation 2. ligand preparation 3. gridbox construction 4. map calculation 5. docking calculation 6. analysis In tutorial of molecular docking on known systems is considered. We know in advance where ligand binds to the protein. But what is the step-by-step algorithm of non-directed docking? And I have no prior knowledge. I think I need to create a gridbox as large as possible (126x126x126, 1 A). If the protein does not fit entirely in the gridbox, then move the center of the gridbox so as to capture the entire structure. That is, at the first step of molecular docking I will have several gridboxes created and calculated. Then I will gradually refine the gridbox values. For example, the next step will be for 126x126x126, 0.375 A maps. And so repeat until the map reaches a size, for example, 50x50x50 0.375A. And if my thoughts are correct, this is where my questions arise. 1. Should the maps overlap with each other in order to cover the whole space? 2. How should I decide which regions of my protein is less favorable? So I can further forget about them and focus only on the most favorable? I look forward to your answers and recommendations. Thank you in advance!

Dear researchers,

I am working both in silico and in vivo in my doctoral thesis. In my in silico studies, I do molecular docking and molecular dynamics simulation and analyzes are performed on the protein. However, I am working on gene expression profiling in vivo. However, the gene I am working on is the gene of the protein I am working on in silico. My question to you is: Is it right to look at gene expression profiling in vivo? Or should I also study protein in the in vivo study? Are there any studies you can recommend on this subject?

Because the organic compund was tested its antimicrobial activity with "Bacillus megaterium" on Kirby-Buyer disc diffusion method.

When searching for the protein structure of "Bacillus megaterium" in RCSB PDB database, exactly it can't find "Bacillus megaterium " in this case which protein should take for molecular docking?

I have attached a screenshot of my search result of RCSB PDB website.

I have conducted virtual screening using Schrödinger on a database of 17,000 molecules. Unfortunately, I cannot use the system with the Schrödinger license at the moment. I am trying to find a way to extract the binding energy from the PoseViewer .pv.maegz file generated by the screening on my local computer without using Schrödinger.

I attempted to convert the .maegz file to .sdf and then extract the binding energy, but this approach did not work. I would greatly appreciate any guidance or suggestions from those who have encountered and resolved a similar issue.

Good day,

I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps recommended for the docking to work with PDBQT files for both the ligand and DNA, but every time i run AutoGrid the window for the process opens for less than 1 second and then shuts down immediately with no output file. i made sure the previous steps were working correctly and to open the ligand and DNA files in their respective input category and the paths for each part in the run window right before the launch have no spaces and are correct. Same problem happens with Autodock.

Does anyone know if there is a fix for this problem?

Thank you in advance.

A molecule shows the -11.6 kcal/mol and second one -8.0 kcal/mol so why molecule (A) revealed higher binding score. Please explain major factor involve in it.

I am a beginner in molecular docking. And I want to know is the active pocket of the receptor the same for all ligands? Or will there be different active pockets for different ligand receptors? I want to do a hydrolase docking with a small carbohydrate molecule, I want to know exactly (or roughly) which part of the active pocket is in (I hope that the binding energy will be lower after docking), so how do I determine which range the active pocket of the receptor is in before docking? Looking forward to your response!

My ligand is a metal complex conatining Ag (Silver). So when i tried to run Molecular docking using Autodock vina as well as PyRx, it shows error as

"Parse error on line 15 in file "Methioninesilver.pdbqt": ATOM syntax incorrect: "Ag" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."

Any necessary recommendation to overcome this error.

Need help regarding Molecular docking for publications, Authorship and due credit will be given. Looking for a purely non funded and academic collaboration, interested people can reach me.

selected 3 compounds I identified from medicinal plant and did some insilico metabolic analysis using an online molecular docking software. This is what I generated.

The Beta sheet- is a Breast cancer type 1 protein molecule

The thick substances are my 3 compounds. Their binding affirnity score range are:

1st one is: -3.9

Second: -4.9

3rd: -4.1.

I can conclude this preliminary results can be a starting point of novel anticancer drugs. Minimal acceptable binding affinity score is -3.2.

I have to perform molecular docking on 2 ligands (A structure-absent in literature and B structure-sourced from PubChem) therefore, is energy minimisation necessary for both?

If a 3D protein is obtained with the inhibitor complex, its wild-type size may change completely. In this case, it seems correct to investigate the binding mode with the inhibitor molecule. If the protein to be investigated has only an inhibitor complex, what protein should I select in the PDB and in my activator molecule research, and what path should it follow?

Hi everyone,

I'm looking for some open source software for molecular docking with constraints based on distances or interactions. Any recommendations would be greatly appreciated.

Thanks!

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Se" -- Add parameters for it to the parameter library first!

How do i handle it? Thanks

Hi

I am practicing molecular docking using PyRx software. In articles, mostly Gaussian software is used to publish the molecular docking of any compound. Can be publish any molecular docking using PyRx (studying docking) and Discovery studio (studying ligand protein interaction, etc). Infect I am a beginner, and it is difficult to use Gaussian.

I have a glycosylated protein and i want to dock it to another protein through the glycans not the amino acids. I have tried HADDOCK but the glycans were broken from each other and from the protein.

Are there specific webservers for docking of glycosylated protein to another protein through the glycan molecules?

molecular docking, aptamer