Membrane anchored protein?

Hi, Is there any way to prove that a protein is membrane anchored/peripheral membrane protein? Any simple trick or any technique will be helpful. Thanks

24 November 2019 1,008 5 View

E.Coli expression strain for expressing mycobacterial membrane protein gene?

Hi, I have cloned some three different constructs which are putative membrane protein of Mycobacterium tuberculosis into pET28a with N-term His tag. I tried to express them in BL21, Rosetta, C41,...

17 December 2018 8,536 2 View

Rosetta (DE3) plasmid throw out?

Hi, I have rosetta (DE3) with incorporation of tRNAs for AGG, AGA, AUA, CUA, CCC, GGA codons on a compatible chloramphenicol-resistant plasmid. I cloned a gene in kanamycin resistant...

30 July 2018 6,527 2 View

Cleaning of Supherose 6 Increase 30/100 GL?

Hi, I feel that my Supherose 6 column is contaminated with some protein because I get pretty clean SDS gel bands after Ni NTA but after SEC I see multiple bands on SDS PAGE. How should I clean...

10 April 2018 1,200 3 View

NO plasmid after isolation?

Hi, I am cloning a 2.8 kb gene into pet28b vector. I did two ligation reaction. In one of them, I did not put insert (only vector and ligase) (control reaction). Then I transformed 10 microlitre...

15 February 2018 1,784 4 View

Is writing a paper a good way to introduce an idea or concept?

Is writing a paper a good way to introduce an idea or concept to be considered by the greater public, industry, etc? I am wondering if sharing an idea through an academic journal may be good way...

01 January 1970 5,527 8 View

No title

01 January 1970 1,741 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 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

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

Ligands with 3,4,5-trihydroxyphenyl group?

Hi In the design of a bidentate ligand with imine group, is it okay to have a 3,4,5-trihydroxyphenyl group in the structure? In other words, does the 3,4,5-trihydroxyphenyl group compete with...

08 February 2021 4,977 7 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View

Can anyone suggest me solution to fix the following problem?

i am working with MD simulations. i am facing error from CGenff server while predicting topology for my ligand file ligand_fix.mol2. error= "readmol2 warning: unrecognized element "Du"readmol2...

21 January 2021 8,290 7 View

Can anyone helps me with Autodock 4.2 scripts error ?

After opening the file, I operate command "Script" --> "Ligand Interactions" --> "Show Ligand Binding Site Atoms" and the warning appears as "This script displays ligands and surrounding...

15 January 2021 5,360 1 View

How to generate topology file for ligand for Gromacs?

Dear all, I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2 When I try to...

22 December 2020 303 4 View