User: maria2019
maria2019 • 130
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Posts by maria2019
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... I am trying to conduct docking of couple of ligands on a protein using Glide and Autodock vina.
When I want to choose the same grid box using the co-crystalized ligand and protein with the 2 tools, I realize that glide and ADTvina give different Grid x,y,z center coordinates!! is that normal??
Sin ...
written 7 months ago by
maria2019 • 130
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... Hi
I have docked 20 ligands to a protein using Autodock vina (with 10 poses for each ligand).
Now I want to choose the **"best" mode for each ligand** and then best ligands (based on the selection of 1). I Know that just these numbers will not be accurate and I will have to look at the 3D as well ...
written 8 months ago by
maria2019 • 130
• updated
6 months ago by
lucaspalmeira.1945 • 10
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... Thank you Kevin, that would be a good start ...
written 8 months ago by
maria2019 • 130
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... Hi,
I have all different kinds of sequencing data (methylation, RNA_seq, ATAC, etc) for only one cancer cell line - no control !!!!!
In fact, I only have "beta value" for methylation, "FPKM" for RNA-seq, etc and no Fold change because there is no Control data.
Is there ANY possible way to integ ...
written 8 months ago by
maria2019 • 130
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... Hi,
I am very new to the molecular docking world. I have done virtual screening on some drugs for some special receptors suggesting the best drug that can be used as an inhibitor. I have used ZINC15 data based ligands, PDB files from Protein Data Bank as receptors and Autodock vina for docking, pym ...
written 11 months ago by
maria2019 • 130
• updated
11 months ago by
Mensur Dlakic • 9.1k
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... Thanks for your comment, Mensur.
I tried that, however, the output format of csv does not give me the name or any other information (even though I check the "name"). The output format of summary table has the names but it does not get extracted as a csv file.
...
written 11 months ago by
maria2019 • 130
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... Hi,
I have downloaded all FDA approved drugs from ZINC data base, about 1600. Each drug has an ID (e.g. ZINC000000000053, which stands for Asprin). How can I convert a list of IDs to the drug name (e.g Aspring), and get some information about the drug? ...
written 11 months ago by
maria2019 • 130
• updated
11 months ago by
Mensur Dlakic • 9.1k
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... Hi,
I am trying to count CpG regions in one of my samples. I know that I can find DMR using DMAP/diffmeth (below is my code).
How ever, I do not know how to find (and count) methylated fragments in only one sample. Any suggestions?
diffmeth -G $ref_path -A 40,220 -U 0.05 -N -I 5 -R $sample1 -R ...
written 13 months ago by
maria2019 • 130
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... I just realized that transpose=FALSE in PCASamples gives the same results as prcomp.
pca <- PCASamples(meth, obj.return=TRUE,transpose=FALSE)
pca ...
written 13 months ago by
maria2019 • 130
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... I have the 'meth' object for my samples and I wanted to see more PCAs.
I realized that PCs from PCASamples are different from what I calculate:
**Using PCASamples():**
library(methylKit)
meth <-readRDS(file="~/files/meth.rds")
pca <- PCASamples(meth, obj.return=TRUE)
pca$x
&g ...
written 13 months ago by
maria2019 • 130
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