User: maria2019

gravatar for maria2019
maria2019130
Reputation:
130
Status:
Trusted
Location:
Last seen:
2 months, 3 weeks ago
Joined:
1 year, 11 months ago
Email:
h******@bgsu.edu

Posts by maria2019

<prev • 77 results • page 1 of 8 • next >
0
votes
0
answers
163
views
0
answers
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 7 months ago by maria2019130
0
votes
1
answer
467
views
1
answer
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 8 months ago by maria2019130 • updated 6 months ago by lucaspalmeira.194510
0
votes
1
answer
248
views
1
answers
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 8 months ago by maria2019130
1
vote
1
answer
248
views
1
answer
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 8 months ago by maria2019130
1
vote
1
answer
452
views
1
answer
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 11 months ago by maria2019130 • updated 11 months ago by Mensur Dlakic9.1k
0
votes
1
answer
420
views
1
answers
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 11 months ago by maria2019130
1
vote
1
answer
420
views
1
answer
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 11 months ago by maria2019130 • updated 11 months ago by Mensur Dlakic9.1k
0
votes
0
answers
212
views
0
answers
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 $sample1 -R ...
methylation dmr dmap cpg written 13 months ago by maria2019130
1
vote
1
answer
472
views
1
answers
Answer: A: Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I just realized that transpose=FALSE in PCASamples gives the same results as prcomp. pca <- PCASamples(meth, obj.return=TRUE,transpose=FALSE) pca ...
written 13 months ago by maria2019130
1
vote
1
answer
472
views
1
answer
Why the PCA results of PCASamples() from methylkit is different from prcomp()?
... I have the 'meth' object for my samples and I wanted to see more PCAs. I realized that PCs from PCASamples are different from what I calculate: **Using PCASamples():** library(methylKit) meth <-readRDS(file="~/files/meth.rds") pca <- PCASamples(meth, obj.return=TRUE) pca$x &g ...
pcasamples multiplepca pca prcomp methylkit written 13 months ago by maria2019130

Latest awards to maria2019

Popular Question 4 months ago, created a question with more than 1,000 views. For Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?
Great Question 7 months 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 8 months ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Scholar 13 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 13 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 14 months ago, created a question with more than 1,000 views. For Strange MT% in 10X scRNA-seq data analysis
Supporter 17 months ago, voted at least 25 times.
Popular Question 20 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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 955 users visited in the last hour
_