Where I can find tutorials for using AMBER molecular dynamics software on supercomputer?

Hi, I am wondering what are the files that should be prepared? how? commands? that enables me to perform MD simulations using AMBER on Supercomputer.

11 December 2019 5,978 5 View

What database or anything else enable me to find the pharmacological actions of certain pharmacophore?

I want to find a database in which i can draw the chemical structure of the core ring and it will give me all the published structures with their biological activity. For example, the...

05 June 2018 1,191 11 View

How can I get a list of FDA-approved drugs of certain category?

I'm wondering how i can find an updated list of FDA-approved drugs for example, proton pump inhibitors, Topoisomerase inhibitors or whatever category.

04 May 2018 4,914 5 View

Any recommendations for highly viscous solvent but should be non-polar and aprotic one?

I'm wondering if you could suggest highly viscous solvent which is non-polar or slightly polar and can't form H-bond interactions. Most preferrably: a glass forming solvent at low temperatures to...

04 May 2018 3,493 4 View

Where I can find a downloadable list for Quartile (quantile) journals ranking?

I'm also wondering is this ranking standard or it differs from website to another.

02 March 2018 6,806 7 View

Some questions regarding proteins sequence and structural comparison?

I hope you can help in these matters. 1) What is the difference between sequence and structural comparison between proteins? 2) Which website or software is good to use to perform this task? 3)...

10 November 2017 9,633 5 View

What are files required to submit GROMACS job on supercomputer?

08 September 2017 2,553 13 View

Intermolecular H-bond bond can be converted into a covalent bond ?

From scientific point of view, if a h-bond is formed as in RN-H.....NAr The covalently bound proton can transfer to other side forming RN.....HN+Ar if it can take place, is there a reference for...

07 August 2017 9,998 6 View

How to purify BSA (Bovine Serum Albumin) for Absorption/Fluorescence spectroscopy use?

07 August 2017 4,999 3 View

Understanding synchronous fluorescence spectrum?

In Synchronous spectrum, both Exc and Fl monochromators are scanned simultaneously. MY questions are; 1) How to determine delta wavelength 2) if delta wavelength is 20nm, does it mean the data...

06 July 2017 4,018 4 View

Buffer to disrupt platelet alpha granules for PF4 quantification?

Hello! I want to quantify by ELISA the secreted (from platelets poor plasma) and the non-secreted (from platelet lysate) PF4 before and after TRAP stimulation. I will use the ELISA from R&D...

03 March 2021 1,499 2 View

Buffer Exchange using column packed with sephadex G-25 effect on protein concentration?

Hello, If i am doing a buffer exchange for an antibody of 1mg/mL, does the elution lose protein in the process of buffer exchange? For example, if i flow through 500 uL of 1mg/mL sample, and...

03 March 2021 6,299 3 View

How optimize the Size Exclusion Chromatography?

Hello! I'll do a size exclusion chromatography, but I only have an open column, and I'll perform the peptide extraction from yeast, using buffer lysis (sodium phosphate 50 mM/NaCl 30 mM/DNAse and...

01 March 2021 2,215 2 View

Why are my bands weird in this Agarose gel?

Can someone please give me some possible things that could go wrong? Here is my recipe: 0.5g Agarose 50 mL of TAE 1x 1 uL ethyl bromide. Gel was run at 100V for 1 hour. The buffer used is also TAE.

01 March 2021 9,952 3 View

What do I do with DLS peaks that are from the buffer?

I'm looking at the aggregation of my protein sample using DLS. Unfortunately, my buffer (20mM HEPES) also results in a set of peaks. These are at approximately 1 and 1000 d.nm. The lowest peak...

01 March 2021 9,015 2 View

What is the most suitable resuspension buffer for TCA/acetone precipitated protein?

I need to extract protein from fermented carbon sources for Bradford assay. Most researchers experiencing insolubility of pellet in resuspension buffer. Please assist me to select most suitable...

26 February 2021 7,129 3 View

What urea buffer can i use for biotagged protein extraction from streptavidin beads?

Hi all, I have been doing research on biotagged LDB1 proteins in Mel cells. I purify the proteins using M280 streptavidin beads. The yield is very low so I've been trying to optimize it by...

24 February 2021 5,749 3 View

Cloudy/high background western blot - can anyone help me?

Hi everyone! I try to detect VDR protein (~48 kDa) using Western Blot. After SDS-PAGE using 10% MP TGX Stain-Free Gel from BioRad I transferred the protein onto an metOH activated PVDF membrane...

23 February 2021 6,266 3 View

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22 February 2021 9,932 11 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