Which software is best for identifying hydrogen bonds and salt bridges in protein-protein dock complexes?

12 June 2022 0 5K Report

pdbsum can generate and identify the h-bonds and salt bridges for you but most of the time i face diificulties with uploading file to pdbsum. if any of you fallow researchers knows about about a good software plz comment.

Badges
Science topic

More Muhammad Adnan Ali's questions See All

PDBsum generation is showing error while uploading a docked complex. What should I do?

While uploading a docked complex (.pdb) onto the PDBsum generation, it shows the following - Uploaded file contains invalid residue names. Please check that your PDB file conforms to correct PDB...

11 June 2022 465 1 View

Basis set and input instruction to calculate HOMO and LUMO using Orca for Imidazolium based organic salts?

Hey there, As a synthetic chemist delving into theoretical calculations for my imidazolium-based organic molecules, I would greatly appreciate any guidance on the appropriate input instructions...

09 August 2024 5,444 7 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View

Why results of ROS flurescence are negative as there was no bacteria within?

Hello. I am working on ROS production of two systems: system A is cerium oxide and hydrogen peroxide, system B is cerium oxide nanoparticle, hydrogen peroxide and potassium bromide. I did some...

04 August 2024 5,974 3 View

How to Transform my handy-wavy explanation of why group I/II metals oxides in aqueous solution are basic into a rigorous argument?

I heard an explanation about something being a better proton acceptor or lone pair donor but that doesn't make sense. I couldn't explain in in terms of acid-base theory. The hand-waving way I saw...

03 August 2024 9,918 0 View

What is the ionic radius of Hydrogen anion? And how to know the exact ionic radii of the elements?

I'm trying to calculate the tolerance factors of the hydride perovskite and the value calculated by me and the reported values are contradictory. Need more clarity in using the correct ionic radii...

01 August 2024 2,614 1 View

Is the mentioned CV graph a valid one as this graph have only one peak prominent (reduction)?

I have used Prussian blue nanoparticles as a redox couple. The PBNPs have been made using only one salt precursor. Also, during scan rate studies, a small oxidation peak can be consistently found...

31 July 2024 9,697 0 View

How to make the concentration measurements for the hydrogen absorption/desorption in the metal hydride?

Hello Everyone! I am trying to create a metal hydride system where I am trying to create a temperature control with the emphasis on measuring the concentration of the hydrogen with the hydrogen...

29 July 2024 7,577 2 View

How to remove/ replace trifluoroacetate countertop after deprotection?

After deprotection of the tert-butyl ester to generate the carboxylic acid in chloroform with TFA, my compound‘s pyridine moiety forms a TFacetate ammonium salt (small molecule drug, not a...

29 July 2024 9,753 3 View

What change would occur in physics if the three different sizes of the proton and the two sizes of the deuteron accepted as new physical constants?

For people today, the enigma of the size of the proton still remains enigmatic. However, being myself a researcher in new physical theory which makes it possible to extend the different standard...

28 July 2024 7,823 1 View

What is the right voltage sweep direction for characterization of HER kinetics?

In general, when performing a Tafel analysis for corrosion resistance measurements, a line voltage scan is performed from say -250 to +250 mV vs. OCV at low scan speed around 0.125 mV/s. However,...

25 July 2024 7,982 3 View