Alvea Tasneem

15 Questions 19 Answers 0 Followers

Questions related from Alvea Tasneem

Webserver for identifying activation and repression of TFs, genes, and miRNAs?

Hello. Is there any webserver where I can input a set of transcription factors, genes, and miRNAs, and it can provide me with statistical data on how TFs either activate or repress genes and...

19 May 2024 5,804 1 View

How to perform protein-ligand simulation on CYP51 protein with a heme group using gromacs?

Hello, I want to perform 100ns GROMACS simulation using CHARM27 force field on a protein-ligand complex where my protein is CYP51 (PDB ID: 5V5Z) which contains a heme group covalantly bonded to...

27 December 2023 9,224 2 View

How to solve the error in gromacs "Warning: Only triclinic boxes with the first vector parallel to the x-axis are supported" ?

Hello, I am getting the error below almost at the end of the simulation performed using gromacs 2023.1 . I am sure I did not encounter this problem before with the same input files. This has just...

09 October 2023 5,404 0 View

How to solve the error "unbalanced atom charge" in OSIRIS property explorer??

Hello, I need to analyze the pharmacokinetic properties of my compound using the OSIRIS property explorer. The compound's SMILES ID is: C[N+](C...

13 August 2023 5,241 0 View

How to solve the "Possible problem with molecular topology file in ligand" error in SwissParam?

Hi. I am trying to create ligand topology and parameter files using SwissParam webserver. I followed all the steps to create the .mol2 file available in SwissParam page:...

03 August 2023 7,282 5 View

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

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...

04 April 2023 4,502 3 View

How can I calculate the Boltzmann Weighted average for thermodynamic properties?

Hello, Is there a way to calculate the Boltzmann weighted average of thermodynamic properties calculated using the hsa_gist command of the SSTMap tool? thank you

12 March 2023 8,810 1 View

Any tool on how to calculate grid inhomogenous solvation theory for hydration site in MD simulated structures?

Hi, Are there any freely available tools/software to calculate GIST? especially for Charmm, NAMD, Gromacs input files... Thank you.

15 January 2023 6,101 0 View

How can I download natural compounds from ZINC15/ZINC20 database?

Hello, I want to download all the natural compounds from ZINC15 or ZINC20 database (either smi, sdf, or mol2 files). https://zinc15.docking.org/substances/?page=1...

03 January 2023 8,200 9 View

How to compile all the individual ligand out files in 1 csv file and extract binding energy and rmsd values to excel sheet?

Hello! Since the latest version of Autodock Vina does not support the generation of the log files, I am finding it very difficult to perform virtual screening of multiple ligands with a single...

03 November 2022 7,143 0 View

How to prepare alphafold predicted protein structure as receptor for virtual screening and molecular docking?

Hello everyone! I have an anti-viral drug target structure with 1087 amino acid residues which are predicted by alphafold. I wanted to know how can I prepare this alphafold predicted protein...

01 September 2022 7,489 11 View

Is there any TCL script program to identify specific MD water molecules forming hbond with certain residues in every frame upon selection?

Hello, I need to check which water molecules (MD simulations) with their specific water IDs are coming at the catalytic pocket of my protein within hydrogen bond distance in 500 frames, i.e., in...

31 January 2022 8,764 2 View

How to minimize the standard deviation of protein-ligand complex using mmpbsa (CaFe 2.0 vmd plugin) using namd?

Hello, I wanted to know how can I minimize the standard deviation (SD) of my simulated protein-ligand complex of 50ns using MM/PBSA method of Cafe 2.0 plugin of VMD plugin using NAMD. I have tried...

11 December 2020 8,296 1 View

How can I calculate RMSD per residue of a protein in VMD?

Hello, I have ran MD simulation using NAMD and CHARMM36 forcefield and want to calculate RMSD values of each residues in a protein. Is there any tcl script that i can use in VMD? I appreciate your...

02 November 2020 8,366 7 View

What is the configuration file for blind docking using PyRx for multiple ligands?

I am trying to run blind docking with multiple ligands and one macromolecule using PyRx but somehow i am getting poor binding affinities. What is the configuration file for blind docking in PyRx...

02 April 2019 2,282 3 View