[ccp4bb] Multiple ligand simultaneous docking

Greetings! I am learning the concept of multiple ligand simultaneous docking and would like to know if there is any standard protocol for the same. Thanking you in advance, With regards, Thripthi Shenoy. To unsubscribe

[ccp4bb] Positive Docking Scores

Greetings to all! I have docked a few compounds with a protein using AutoDock Vina. The compounds are exhibiting positive binding energies even though they are docked in the active site. I would be grateful for any help regarding the same. Thank you, Regards, Thripthi. ##

[ccp4bb] Manual setting of config file in PyRx

Greetings to all. I am screening around 500 compounds using Pyrx. I wanted to know if it is possible to use my old Config file without manually moving the grid box in PyRx. Any assistance in this regard would be very helpful. Thank you, Regards. Thripthi S.

[ccp4bb] Manual setting of config file in PyRx

Greetings to all. I am screening around 500 compounds using Pyrx. I wanted to know if it is possible to use my old Config file without manually moving the grid box in PyRx. Any assistance in this regard would be very helpful. Thank you, Regards. Thripthi S.

[ccp4bb] Glide fails to generate accurate docking pose

Greetings to all. I am trying to dock a co crystallized ligand using GLIDE. The co crystallized ligand is a big molecule with multiple rotatable bonds. GLIDE is unable to regenerate the ligand pose. I tried limiting the rotatable bonds, but in vain. I would be grateful to receive any advice or sug

[ccp4bb] Regarding MM/GBSA binding energy of docked complexes

positive while the docking scores are negative. I tried to find and rectify the mistakes but in vain. I do not understand how to proceed further. Any assistance in this regard would be very beneficial for me. Thanking in advance, With regards, Thripthi Shenoy

[ccp4bb] Glide grid box

Greetings to all! I am trying to generate a grid box over the co-crystallized ligand in Maestro. However, the ligand is not being detected and the gridbox is generated outside the protein-ligand complex. I tried all possible ways, but in vain. Any suggestions in this regard would be very helpful t

Re: [ccp4bb] Autodock vina docking results

, Bareilly-243123, > UP, India. > > Alternate E-mail: subhomo...@invertisuniversity.ac.in > > > https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokJ > Web of Science Researcher ID: AAC-9193-2021 > <https://publons.com/researcher/AAC-9193-2021/

[ccp4bb] Autodock vina docking results

Greetings to all, I have performed docking through Glide and Autodock vina for a protein for which the active site has been taken from the literature. Glide is able to dock the compounds correctly in the active site whereas autodock vina does not dock the compounds within the specified site. I hav

[ccp4bb] Error in defining the binding site

Greetings to all! I am learning and trying to run a docking program using Schrodinger Maestro. While identifying the binding site for the co-crystallized ligand, I am facing an error that states "Ligand misidentified. No receptor atoms left after masking the ligand." I am clueless how to proceed f

[ccp4bb] Rigid ligand docking

Greetings to all. I am a student trying to understand various aspects of molecular docking. I have tried self-docking for a few proteins co-crystallized with larger molecular weight ligands with torsions more than 30. I tried reducing the torsions of ligands through AutoDock Vina since flexible li

[ccp4bb] Docking analysis

, but do not have a control ligand to compare the results. I would be grateful if I could get any suggestions on how I should proceed with the analysis. Thanking in advance, With regards, Thripthi Shenoy. To unsubscribe from

[ccp4bb] SWISSDOCK results

.pdb files? Thank you all in advance, Thripthi Shenoy. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to member

[ccp4bb] Protein Ligand Interaction Profiler

Greetings to everyone, I am trying to study the molecular interactions of some ligands using Protein Ligand Interaction Profiler (PLIP) and it shows errors like this. "Sorry! An error occurred. Please try later or contact our system administrator." I would be grateful if someone could help me out

[ccp4bb] Calculation of active site and ligand area

Hello everyone, I want to calculate the area of the protein active site and the area of its bound ligand in the active site. I tried with SASA calculation but the area of ligand turned out to be zero. Any suggestions on how to proceed would be appreciated. Thanks and regards, Thripthi S. #

[ccp4bb] Binding affinity in AutoDock Vina

I am performing docking studies for some of the protein structures from PDB using AutoDock Vina. Some of the ligands are giving binding energy as positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to my knowledge. I would be grateful if someone could explain to me the reason fo

[ccp4bb] Calculation of surface area of active site

Greetings! I am currently trying to find the surface area of a protein active site. I tried with SASA but could not succeed. I wish to find the area of ligand and the area in the active site it is binding to. I would like to have some suggestions to proceed. Thanking in advance, Thripthi S. ##