User: prasundutta87

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Posts by prasundutta87

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Comment: C: Molecular Docking, More Receptors, Single ligand
... Docking and molecular dynamics simulations are separate algorithms and are done separately. You dock first to get a static interaction and then perform molecular dynamics to check if the interaction persists with time (superficial definition). You asked if docking can be done with two receptors s ...
written 4 days ago by prasundutta8770
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Answer: A: Molecular Docking, More Receptors, Single ligand
... What do you mean at the same time? Do you want to know if it has more affinity towards the MHC or the T-cell (receptor)? You have to perform your docking procedure separately for each receptor molecule and compare their binding energies to make the comparison. I don't think its technically possible ...
written 4 days ago by prasundutta8770
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Answer: A: GATK ASEReadCounter: Downstream analysis for identifying allele specific express
... ASEReadCounter is doing what it says its doing..just counting the ref and alt reads per allele.. A chi square test or a two sided binomial test is fine for determining locus based ASE..for gene based there are other methods..you can get more information from this paper- http://ieeexplore.ieee.org/s ...
written 6 days ago by prasundutta8770
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Comment: C: how to measure gene expression level using third sequencing long reads (for exam
... Good question..As far as I understand, pacbio reads are long reads that are better than short reads (like illumina) as they produce less gaps. PacBio reads are mainly used for genome assembly purposes and do not need or have much depth which is a necessity for gene expression/variant calling studies ...
written 7 days ago by prasundutta8770
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Comment: C: expression to networking
... Biolayout 3D has been deprecated and is no longer supported..Miru (https://kajeka.com/) is its successor and is faster and more optimised than its predecessor.. ...
written 8 days ago by prasundutta8770
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Comment: C: Ligand Docking Simulation Programs
... I can suggest one thing..check out this Galaxy instance: http://mpds.osdd.net/ Go to data analysis-->Docking and follow the instructions.. All the required steps are performed internally and you don't require to install any tools or binaries or think about software versions anymore..Vina is imp ...
written 8 days ago by prasundutta8770
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Comment: C: Ligand Docking Simulation Programs
... autodock Vina is different from autodocktools and not part of it so you may not face this particular python issue there..check this website: http://vina.scripps.edu/ and its FAQ part about the differences..it has its own binaries.. You are right that its a Python version issue and I faced it long b ...
written 8 days ago by prasundutta8770
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Comment: C: Ligand Docking Simulation Programs
... You can use autodock Vina...its very fast and is available in binary version.. ...
written 9 days ago by prasundutta8770
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Comment: C: Energy minimization of protein
... Swiss-PDB Viewer can be used for energy minimization- http://spdbv.vital-it.ch/energy_tut.html Reason mentioned in the tutorial.. ...
written 9 days ago by prasundutta8770
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Answer: A: Ligand Docking Simulation Programs
... Are you referring to molecular dynamics simulations that is performed after docking experiment? ...
written 9 days ago by prasundutta8770

Latest awards to prasundutta87

Scholar 12 days ago, created an answer that has been accepted. For A: Retrieving SMILES using CAS or SAMPLE ID or SAMPLE_NAME
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation

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