How do we have to incorporate metal in model structure of protein? is there any option in autodock? i want to do docking small ligand along with metal?
take a look at
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
RNA structure prediction
01 February 2018 4,000 0 View
why only these denaturants used why not others can anybody give explanation for this?
01 February 2017 6,630 0 View
I have done molecular docking of one protein and ligand but i don't know how do i have to calculate free energy in between these two molecules? can you suggest anyone commands related to this?
11 December 2016 2,214 1 View
i am getting big crystals by increasing MPD from 40% to 60%, is the possibility of getting mpd crystals or they are protein crystals, those crystals are not well formed plz give suggestions.
11 December 2016 6,884 1 View
Please can any one suggest me preparation or how to dissolve gingkotoxin for my experiments?
09 October 2016 4,949 4 View
i have protein dimer sequences of chain A and B, how can i model these two sequences? i want to get as dimer. is there any software ? can you suggest?
09 October 2016 7,125 1 View
I have one transcription factor, so how do i have to do dock with DNA? how can i create PDB file of DNA? what is the procedure for simulation in gromacs? can you suggest anyone?
09 October 2016 1,172 0 View
i have modelled one protein by using modeller, after docking protein with suitable ligand, it is interacting with five amino acid residues, then i submitted that complex to 20 ns simulation...
08 September 2016 9,778 3 View
Basically how many nanoseconds we have to use for protein simulation? i used 20 ns for modeled structure, is it sufficient or shall i increase the time? can you suggest anyone?
08 September 2016 5,630 8 View
I'm working on selecting antibodies against a recombinant protein that has a His-tag. My idea is to first bind the recombinant protein to a HisTRAP column and then use this column for an affinity...
07 August 2024 505 3 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
Molecular docking software/ websites?
02 August 2024 8,704 7 View
Is it the "elution buffer" or the "dialysis buffer"? Note: I'll be using NanoDrop OneC
01 August 2024 967 3 View
Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...
31 July 2024 9,892 4 View
When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!
29 July 2024 488 0 View
Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....
29 July 2024 5,007 0 View
I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...
28 July 2024 366 3 View
I cannot confirm cell surface protein expression by flow cytometry even after transfection and antibiotic selection of cells. Does it take long for proteins to express on the cell surface? the...
28 July 2024 3,178 3 View
Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...
28 July 2024 2,136 4 View