Thiliban Manivarma

5 Questions 5 Answers 0 Followers

Questions related from Thiliban Manivarma

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

05 August 2024 1,069 2 View

I have been trying to understand the Implicit Liagnd Sampling (ILS) using volmap packages in the VMD. Could anyone guide me, how to start with it?

I have been trying to understand the Implicit Ligand Sampling (ILS) using VMD/NAMD to understand and study oxygen tunnels in the protein of interest and I have all the parameter files and all the...

25 September 2023 8,984 0 View

I have a dataset of inhibitors against ferroptosis programmed cell death which I curated from chEMBL, how do I get the top 10 inhibitors using ML/AI?

Hello people, I have a dataset of inhibitors as binary labels ( Zeros - Inactive , Ones - Active ). I have my ML/AI model working, now I would like to know how many are the best inhibitors out of...

19 September 2023 1,321 4 View

How do I solve this Ligand's coordinates while generating psfgen in NAMD ?

Hello everyone, I have been building my system ( protein-protein complex ) with different ligands in it, after building I could see some strange lines which are pointing towards the center, I do...

28 February 2023 710 1 View

How do I collect Protein-Protein residue pairs interaction feature from PDB file to build a dataset for Machine learning analysis?

I have a protein-protein interaction complex ( Hetero protein ), I need to collect the information of amino acid pairs. Thank you, any suggestions would be appreciated.

13 May 2021 395 3 View