Hi all,
What is the best free software/code to calculate free energy Perturbation (FEP) analysis on receptor-ligand complex?
FEP can be performed using GROMACS.
http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf
Thanks you Dmitri, it was a great help.
Q: https://github.com/qusers/Q6
Thank you so much dear Samee,
I need to to do FEP analysis for a set of thousands congeneric ligands against a receptor. Which tool would you recommend?
Perfect, many thanks Samee.
I would like to interpret a trained model for an image recognition system and understand which part of the feature vector(the last layer that I am using for cosine similarity or matching with...
01 January 2024 149 1 View
Ratio of horizontal to vertical permeability of compacted clay.
10 September 2023 4,347 0 View
I mean, which physiological or immunological parameters/markers that I need to study to know the effect of using immunotherapy in the patients with lung cancer? Any suggestion for research would...
02 August 2023 4,079 3 View
It would be preferred if the book covers all aspects of biological wastewater treatment including but not limited to chemistry, microbiology, resources recovery, and characteristics of bioreactors.
05 February 2023 8,142 8 View
What does it mean if the status date changes while the status remains with editor?
09 January 2023 8,182 2 View
Hi, Imagine that you are going to sample a protein conformation (consists of N atoms) using Monte Carlo and Molecular Dynamics simulations, independently. For the MD simulation, the phase space...
06 December 2022 318 6 View
I have two small characteristic peaks in the NMR spectrum showing negative integration values. I would appreciate it if you could share your opinion.
28 November 2022 9,933 2 View
previously I used the zinc database and DrugBank for this purpose but today appears this property was canceled.
28 August 2022 5,407 0 View
Hi all, What is the best way to draw a FES diagram for a metadynamics simulation with 3 CVs? I know that it is still possible to draw 2D FES diagram with two CVs and project the Free energy...
11 December 2021 908 4 View
hi.. if i mix AgNPs powder in D.W and then pour 20 ul of this mixture on each filter disk 6mm ? what is the best technique you recomended?
21 October 2021 4,125 3 View
"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....
10 August 2024 8,621 1 View
How to develop investments in renewable energy sources?
08 August 2024 5,112 3 View
Hello experts, Does anyone know any free software about retention index prediction ?
08 August 2024 7,403 2 View
Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...
06 August 2024 1,989 3 View
Please can anyone support with the survey questions based on RQ measures and propose how to do it in FMCG industry and include as well the role of brand equity Thanks
06 August 2024 949 0 View
How to design VN primer to attach with universal reverse primer
05 August 2024 2,116 3 View
I have an antibody binding generic protein and I need to compare its activity in a free and immobolized form. I understand that there are a number of methods to determine Kd value of a free...
05 August 2024 5,311 0 View
kindly reply me. Thanking you in advance.
05 August 2024 7,727 4 View
why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...
03 August 2024 3,589 3 View
I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...
03 August 2024 1,370 1 View