I want to know that whether we can find solubility of a protein by computational tools??
Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance.
03 April 2019 6,340 2 View
Hi all, I have gauss view (6.0.16) and gaussian16W for microsoft windows. I want to generate the wfn file. I have tried specifying of C:\path\molecule.wfn in molecular specification section...
11 December 2018 7,496 0 View
Hello everyone, I have run optimization of protein-ligand complex using QM/MM in gaussian. I did not find any criteria to find how much time will be taken to complete this job. Is there any...
10 November 2018 9,302 0 View
Hi everyone, We have HP server consist of 160 processors on 80 cores (i.e. each core has 2 processors). We want to utilize this server for molecular dynamics work. So we want to combine like 60...
02 March 2018 2,726 0 View
Hi everyone, I have to do Molecular Dynamics Simulations of a FE2S2 center containing protein. I need to generate the FE2S2.mol2 and FE2S2.frcmod files. I have used the antechamber and parmchk...
11 December 2017 1,949 0 View
Hi everyone, I have run the molecular dynamics of FES cluster containing protein in GROMACS. I got the error that FE and FES are not found in the amino acid database of force field. What can i...
10 November 2017 9,911 0 View
Hi everyone, I have done molecular dynamics simulation of protein with ligand in GROMACS. I am not much aware of occupancy of hydrogen bonds in complexes. What does occupancy of hydrogen bonds...
09 October 2017 2,775 0 View
Hi, I have run the MD of a protein by using Gromacs. I have generate the number of hydrogen bonds between protein and ligand by following command:- gmx hbond -f md_0_1.xtc -s md_0_1.tpr -num...
08 September 2017 981 0 View
Hi everyone, I have modellled a protein by phyre. I got the 5 residues in outlier, so I tried modloop to build loop. When I used this model in gromacs for MD by CHARMM37. I got this error:- Atom...
06 July 2017 9,076 0 View
Hi all, I have to do molecular dynamics of a protein. it is trimer of dimer. It has total 6 chains Although in dimer both chains have same amino acids. It has 6 ligands. Ligand interact via...
06 July 2017 6,125 6 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
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05 August 2024 4,407 0 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
Hello everyone, I am try to understand the differences interaction between insoluble and soluble polymers in water with metal ions and how theit charge density (of metal ions) affect the interaction.
29 July 2024 6,350 3 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
Dear all: I am modifying Bismuth Tungstate with Hematite (Fe2O3), so I would like to know about how much Iron(+3) can form a solid solution in a Bismuth Oxide matrix. Best wishes Marco
29 July 2024 2,163 1 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