How can I interpret HEX server protein-protein docking results?

More Kishna Vijayaraghavan's questions See All

How can we do a Reverse Technology Process?

Target identification -> HTVS -> Glide XP -> e-pharmacophore mapping?

03 April 2014 5,186 0 View

How can I predict the IC50 value for a ligand with the help of an occupancy value?

I have the occupancy value (Binding area value of my protein docked with my ligands). Can I predict the IC 50 value?

03 April 2014 2,856 3 View

Does anyone know how PPAR-Gamma is related to Type II Diabetes?

see above

03 April 2014 337 3 View

Can anyone tell me what K-mean clustering means?

In what bases does K-mean clustering separate data?

02 March 2014 7,431 6 View

How can I generate a heatmap using the docked file data I have collected? .

Which server can use for heatmap generation? I have the docked file data (3 PDB files).

02 March 2014 9,878 0 View

Is there any software or online server to do cluster analysis ?

Cluster Software programs: I have a set of compounds ( say 10000 ); I want to cluster them or group them into certain properties( say structures). How can I group them? Is there any software or...

01 February 2014 2,048 3 View

Can I use e-Pharmacophore on any web server?

see above

01 February 2014 4,331 1 View

Does anyone know how to view the alignment results in ESPript?

I have given the clustalw (*.aln file) as input and given the submit button,but it doesn't shows any alignment result or images? How to view the output files?

01 February 2014 9,730 3 View

Can anybody provide a small paragraph about e-pharmacophore?

e-pharmacophore explanation.

01 February 2014 7,892 1 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

I'm a student and I have to produce a cell line with a knockin for the NRF2 gene with GFP. I have to put a promotor in front of the GFP because the gene will be too far away from the promotor of...

28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

I have used an AllPrep DNA/RNA/Protein Mini Kit QIAGEN kit to extract RNA and protein from my samples. At the end of the protein purification, I resuspend my protein in 5% SDS. Will these samples...

28 February 2021 7,370 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

How to replicate the well conditions of a crystal hit with 20%(w/v) isopropanol?

I had a crystal hit in a well with 0.1M HEPEs pH 7.5, 10%(w/v) PEG 4000, and 20%(w/v) isopropanol. Why is isopropanol in w/v here if it's just solvent? How do I recreate this well condition?

25 February 2021 9,761 1 View

Problem with ligating 2.8 kb insert into 8.5 kb plasmid?

I am trying to clone 2 copies of the same mammalian gene into the pSF-CMV-Ub-Puro Ascl (contains HindIII, KpnI and NheI cut sites) plasmid. This is what the final product is supposed to look like...

24 February 2021 6,310 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

Can I use a protein-devoid condition as my negative control in ELISA?

Hello, I am running a sandwich-type ELISA where I am trying to inhibit a protein-protein interaction using small molecules. For each experiment, I determine my Z' (Z-prime) to determine the...

23 February 2021 7,429 1 View

Siva Kumar

The docked file is *.pdb file. It contains many docked positions, in order to identify the docked position with lowest energy value ("highest negative"), you can refer *.hex file. After refering the file, you can choose the corresponding pose in hex software. You can also manually pick the pdf pose file from the *.pdb file by using the microsoft office tool.

Kishna Vijayaraghavan

Thanks Neeraj Brother and Siva Kumar sir :)