How can we do a Reverse Technology Process?

Kishna Vijayaraghavan @Kishna_Vijayaraghavan

04 April 2014 0 5K Report

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

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

I've got two files, *.hex and *.pdb files. I want to see the interactions between those two proteins. How can I see it?

03 April 2014 10,023 2 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

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

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...

08 February 2021 7,426 3 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Schrodinger Desmond runs fine on one GPU, but crashes on other GPU?

Hi, We are having issues using Desmond on our workstation. Simulations run fine on one of our gpus ("Gpu0") but crash consistently on the other gpu ("gpu1" - which is also set up as the display...

01 February 2021 5,866 3 View

Qiime2- No reads passed the filter. How to set the trunc value?

Hi, I am working on some 16S sequencing data, and seems some of them are low quality. I am not sure how to set the trunc value in dada2. qiime dada2 denoise-paired \ --i-demultiplexed-seqs...

30 January 2021 6,213 3 View

Which software to use to statistically analyze Telomere Length_TRF_Southern Blot?

I am trying to measure telomere length in an ant species using the TRF method, which is a Southern blot technique. Currently, I am struggling with analyzing the images and would appreciate any...

29 January 2021 604 3 View

MHC Rabbit Genome Annotation? Domain annotation of each MHC Rabbit Gene?

I want to find a database(s) or a method where I can find and bulk download all the rabbit MHC genes and domain annotation. In humans using Ensembl, all MHC genes have names and domains but in...

28 January 2021 7,722 2 View