User: maria2019

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maria2019100
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Posts by maria2019

<prev • 77 results • page 1 of 8 • next >
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Why Grid centers are different between Glide and ADTvina for the same Ligand-protein structures
... 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 ...
glide autodock vina vina grid docking written 4 weeks ago by maria2019100
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How to chose best ligand option based on affinity and RMSD from Autodock vina docking results?
... 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 ...
autodock vina binding affinity docking rmsd ligand written 6 weeks ago by maria2019100
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Comment: C: how to analyze/integrate methylation "beta value" and RNA-seq "FPKM" data from o
... Thank you Kevin, that would be a good start ...
written 6 weeks ago by maria2019100
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how to analyze/integrate methylation "beta value" and RNA-seq "FPKM" data from only one cell line
... 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 ...
beta value omics fpkm integration rna-seq written 6 weeks ago by maria2019100
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Which journals accept molecular docking analysis using Autodock vina
... 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 ...
journal autodock vina molecular docking ligand written 4 months ago by maria2019100 • updated 4 months ago by Mensur Dlakic6.0k
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Comment: C: Zinc data base drug ID to drug name convertor
... 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 4 months ago by maria2019100
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Zinc data base drug ID to drug name convertor
... 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? ...
drug name id to name zinc database written 4 months ago by maria2019100 • updated 4 months ago by Mensur Dlakic6.0k
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how to get methylated fragments (CpG regions) for only ONE sample using DMAP
... 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 $sample1 -R ...
methylation dmr dmap cpg written 6 months ago by maria2019100
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Answer: A: Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I just realized that transpose=FALSE in PCASamples gives the same results as prcomp. pca <- PCASamples(meth, obj.return=TRUE,transpose=FALSE) pca ...
written 6 months ago by maria2019100
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Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I have the 'meth' object for my samples and I wanted to see more PCAs. I realized that PCs from PCASamples are different from what I calculate: **Using PCASamples():** library(methylKit) meth <-readRDS(file="~/files/meth.rds") pca <- PCASamples(meth, obj.return=TRUE) pca$x &g ...
pcasamples multiplepca pca prcomp methylkit written 6 months ago by maria2019100

Latest awards to maria2019

Great Question 29 days ago, created a question with more than 5,000 views. For What is the right illumina universal adapter sequence for trimming paired-end reads?
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Scholar 6 months ago, created an answer that has been accepted. For C: What is the best R package to plot eye catching 3D PCA plots?
Scholar 7 months ago, created an answer that has been accepted. For C: What is the best R package to plot eye catching 3D PCA plots?
Popular Question 7 months ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Supporter 10 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For What is the right illumina universal adapter sequence for trimming paired-end reads?

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