Omar A. Soliman

11 Questions 5 Answers 0 Followers

Questions related from Omar A. Soliman

Whats is the difference between interaction entropy approximation and c2 entropy approximation?

I carried out MMPBSA calculation using gmx MMPBSA module and allowed for entropy calculation through mmbsa.in the parameter file. it yielded two values 1- interaction entropy approximation 2-c2...

12 August 2024 8,939 0 View

Requesting information regarding B-Cell Epitopes immunogenicity Prediction, Can you suggest bioinformatics/immunoinformatics tools?

Hello there, I'm searching for reliable bioinformatics/immunoinformatics tools for predicting the immunogenicity of B-Cell Epitopes. Your expertise is invaluable! Could you kindly recommend any...

18 August 2023 1,771 1 View

Why cluspro not showing reproducible poses?

Hello there, I have carried out Protein-Protein docking using cluspro on 2 different receptors, with the same protein with slight mutations between them. the first receptor showed strong...

20 December 2021 5,987 2 View

A Method to Assess Protein-Protein Energetics?

Hello there, I have a couple of Protein-Protein complexes; an output of a docking procedure, I want to assess the Electrostatic potential and Van der wall energy of those complexes. So is there...

03 December 2021 6,391 4 View

Is there a way to model Multi-mimer Homology modelling using Chimera (MODELLER)?

Hello there, I am trying to model SARS CoV2 S protein using Chimera utilizing Modeller, The problem is, it's not suited for multimeric homology modeling. I have seen this tutorial on their forum...

19 September 2021 7,684 3 View

Is there a way to isolate one chain containing two docked protein resultant from Cluspro docking?

Hello there, I carried out Protein-Protein docking using the Cluspro server, the problem is that Cluspro provides resulting models as one combined PDB, so I am asking I there is a way I can...

15 September 2021 8,123 2 View

MOE protein-protein error: Ligand vector exceeded?

Hello there, I am trying to run a protein-protein docking using MOE, I have prepared both the ligand and the receptor, and then I open the Docking windows, select the desired residues for both...

07 September 2021 8,538 4 View

Insight on MOE different docking algorthiums and scoring functions?

Hello there, I have attempted a docking Study using Auto dock vina, the results were quite logical and interpretable, yet I wanted to refine them due to high RMSD values, and I wanted a way to...

03 September 2021 6,979 2 View

In MOE Protein- Protein Docking , can ligand and docking site be selected through residues selection?

During MOE Protein Proein docking, can the ligand the residue binding side, get selected through sequence editor? I am not using the site finder module , yet I know the receptor docking...

03 September 2021 5,082 0 View

What is the best valid and optimized and productive way to identify binding site of a protein and carry out docking on it via Autdock ?

Hello there, I want to use Autdock for a docking study, I have used it before, yet I recall that the Grid optimizing process with vary vague and I couldn't fully trust it, is there a possible...

31 August 2021 9,916 3 View

What is the reason of high RMSD values when carrying out self-docking via MOE?

hello there, I want to carry out a screening process via molecular docking, I attempt to carry out self docking of the co-crystallized ligand via MOE, that usually yield RMSD values higher than...

31 August 2021 848 2 View