User: dasdevashishdas

gravatar for dasdevashishdas
Reputation:
120
Status:
Trusted
Location:
India
Scholar ID:
Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
3 years, 7 months ago
Email:
d**************@gmail.com

Posts by dasdevashishdas

<prev • 23 results • page 1 of 3 • next >
0
votes
0
answers
420
views
0
answers
Comment: C: Pseudo atom in a cavity
... If you already know the atoms of the opening of the cavity, then select and create a new object (obj1) from action menu. Then place a pseudoatom by pseudoatom StartCavity, obj1 ...
written 10 weeks ago by dasdevashishdas120
0
votes
1
answer
845
views
1
answers
Answer: A: How to set own code to Wizards Menu of Pymol ?
... I know it is nearly 3.5 years! I found the solution. It is "cmd.wizard" wizard distance # launches the distance measurement wizard # set a message cmd.wizard("message", "Hello, I'm a message.") # dimiss the message cmd.wizard() Source: https://pymolwiki.org/index.p ...
written 10 weeks ago by dasdevashishdas120
0
votes
0
answers
343
views
0
answers
Comment: C: Gromacs-Molecular simulation of a protein and ligand
... Please use https://atb.uq.edu.au for generation of itp file. Post the full error for MKTOP. ...
written 7 months ago by dasdevashishdas120
0
votes
1
answer
902
views
1
answers
Answer: A: RMSF AND ngmx in GROMACS
... 1. **How to check and visualise the box dimension at protein ligand simulation in GROMACS 5.0.4 ?** It depends on which format (PDB, GRO and XTC) you want to use. For visualization: Use VMD ( www.ks.uiuc.edu/Research/vmd , http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD). T ...
written 7 months ago by dasdevashishdas120
3
votes
1
answer
287
views
1
answer
Why single SNP (rsid) belong to more than one Gene?
... Dear all, I wanted to know the reason why there is more than one gene specified for a single RSid (dbsnp)? eg: For **rs3827295** Gene: **LINC01664** and **CECR6** **rs5751876** Gene : **ADORA2A-AS1 + ADORA2A + SPECC1L-ADORA2A** rs35921388 Gene : **GSTTP1 + GSTTP2 + LOC105372959** ...
gene dbsnp snp written 7 months ago by dasdevashishdas120 • updated 7 months ago by WouterDeCoster26k
0
votes
1
answer
508
views
1
answers
Answer: A: Ligand topology with gromacs
... **My first question is: is PRODRG the suitable program for generation of small molecule topologies?** No. please use acpype (webapps.ccpn.ac.uk/acpype/ ) or better use ATB (https://atb.uq.edu.au/ only gromos forcefield). For complete list see: http://www.bevanlab.biochem.vt.edu/Pages/Personal/jus ...
written 7 months ago by dasdevashishdas120
0
votes
0
answers
281
views
0
answers
VQSLOD score different for Full and split (by chromosome) BAM file
... Dear all, I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score: **For full : VQSLOD=-6.339e-01** **For split : VQSLOD=-1.472e+00** Does this means splitting the BAM is not correct or is it b ...
vcf gatk written 10 months ago by dasdevashishdas120 • updated 8 months ago by Biostar ♦♦ 20
2
votes
0
answers
312
views
0
answers
What are the adapters in illumina platinium genomes?
... Hello All, I want to know the adapters (if present) in the illumina platinium genomes. The website (https://www.illumina.com/platinumgenomes.html) and the paper (http://genome.cshlp.org/content/27/1/157) doesn't talk about it. Also, is there any specific Cutadapt command, we need to pass to get t ...
adapters assembly sequencing written 12 months ago by dasdevashishdas120
1
vote
2
answers
503
views
2
answers
Answer: A: Predicting the 3D structure of a protein
... You have two option: 1. Consider multiple template and go for homology modelling 2. Do Protein threading prediction (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) ...
written 13 months ago by dasdevashishdas120
0
votes
0
answers
300
views
0
answers
How to benchmark new Blast based annotation tool?
... Dear All, I want to know, the best way to test/benchmark our newly developed cloud based annotation tool? It uses NCBI BLAST+ on our framework in cloud. When we tested it on tomato reference with 34,725 which it finished it in less than 4 hours (which is 12 times faster than without the framework!) ...
next-gen blast written 14 months ago by dasdevashishdas120

Latest awards to dasdevashishdas

Popular Question 7 months ago, created a question with more than 1,000 views. For Any free tool for Calculating Gasteiger-Hückel charges for ligands?
Supporter 13 months ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Next Generation Sequencing for Beginners
Student 2.2 years ago, asked a question with at least 3 up-votes. For Any free tool for Calculating Gasteiger-Hückel charges for ligands?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Using Biopython and BLAST+ to automate de novo viral contig sorting
Scholar 3.2 years ago, created an answer that has been accepted. For A: Using Biopython and BLAST+ to automate de novo viral contig sorting

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1068 users visited in the last hour