How can I automatically screen compounds in a docking library that have made specific interactions with a residue?

24 April 2023 0 10K Report

I'm working on a virtual screen of approximately 8000 compounds, and I need to select only those that interact specifically with an active site residue. However, it is clearly impossible to inspect all these compounds visually. I used the GOLD software for docking, and I would like to know if there is any resource in gold or other software that I can use to select only the compounds that showed interaction with a specific residue.

Thank you for your attention in advance.

Badges
Science topic

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

How to remove the residual PDMS on the silicon mold?

Incompletely cross-linked pdms are difficult to remove.

01 March 2021 798 3 View

Why there are two peaks while using the mie plot of Silver nanoparticle?

Hi, I am trying to learn the theoretical modelling of silver nanoparticle using the Mie scattering theory. After that, I discovered a software named Mieplot developed by Philip Laven, where it...

25 February 2021 7,493 6 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How do I check the quality of my viral RNA prior to metagenomic sequencing?

I am doing metagenomic sequencing without enrichment for an RNA virus. After my RNA is extracted from the blood I am doing library prep with the NEBNext Ultra directional RNA library prep kit for...

16 February 2021 5,101 2 View

Can bio-decomposer be a successful alternative to reduce residue burning?

To maintain the proper crop plan most of the times there is not enough time to make the field ready for the next crop. In this particular context , can bio-decompser be a solution? What about...

16 February 2021 7,068 24 View

How to remove the species data from rda data frame in R (only remain the sites/samples point)?

Dear everyone, When I using the rda function in r, I met this question. As you can see in the figure, there are a lot of deep blue points which refers to the species. But I would like remain...

15 February 2021 8,982 2 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View