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Should energy minimization of native and mutant protein structures be done before RMSD calculation between these two?

rmsd homology energy minimization yasara written 6 months ago by anis.geb.cu • 10 • updated 4 months ago by Biostar ♦♦ 20

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Automation for Energy Minimizing protien structure

energy minimization gromacs protein structure written 20 months ago by yashwanthakumar • 10 • updated 20 months ago by fracarb8 • 50

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Error in MDS of complex

complex gromacs energy minimization written 3.9 years ago by Arindam Ghosh • 340

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What is the basis of inputting the emtol parameter in the minim.mdp?

energy minimization gromacs written 4.1 years ago by syedazeemullah186 • 0

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Forum: Reasons of Doing Energy Minimization and Binding Site Prediction

virtual screening energy minimization binding site forum written 5.3 years ago by sakurashirleyke • 30

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protein ligand docking

protein ligand docking energy minimization written 5.4 years ago by sanbioinfo • 0

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Protein structure distorted after energy minimization using GROMACS

energy minimization written 5.9 years ago by BI • 70 • updated 5.9 years ago by venu ♦ 6.7k

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C: RNA-seq using DESeq2: quality control of replicates using PCA and heatmaps by rpolicastro ♦ 3.2k
If you complete analysis, how many DEGs show up? Since PC1 is nicely separating the samples by co...
C: Extract the overlapping paired-end reads by Carlo Yague ♦ 5.5k
You can select overlapping mate pairs based on the template length (9th) field of SAM/BAM files. ...
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You can't put in gene sequences. You will need to use region/co-ordinate information to pull out ...
C: add sample name to bam header based on bam file name by Pierre Lindenbaum ♦ 133k
http://www.htslib.org/doc/samtools-addreplacerg.html > -R STRING Allows you to specify the re...
C: add sample name to bam header based on bam file name by Ana • 180
I do not want to change the ID, its the same. How can I adjust it?
C: GSVA Error: "Less than two genes in the input expression data matrix" by ivykosater • 0
No particular reason. Here are the first few rows and columns of expr expr Name ...
C: add sample name to bam header based on bam file name by Pierre Lindenbaum ♦ 133k
option `-r "ID:xxxx"` is required.
C: Analyze a gene sequence across the 1000 genomes data by davidenoma • 40
Hi @GenoMax. I intended to find the variations of the particular gene across the different popula...
C: add sample name to bam header based on bam file name by Ana • 180
for file in *.bam; do base_name=$(basename $file .grch37.bam); samtools addreplacerg ...
C: Extract the overlapping paired-end reads by Ar • 1.0k
Thanks! I will try it.
C: Extract the overlapping paired-end reads by GenoMax ♦ 94k
In that case following @lieven's suggestion will allow you to pre-select reads that overlap. You ...
C: How to download triple negative breast cancer RNA-seq fpkm data from GDC. by Jeremy Leipzig ♦ 19k
saw this post mentioned in a DNANexus tutorial https://www.youtube.com/watch?v=1TcvCrszprk

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