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Questions related to Bioinformatics and Computational Biology
I am interested in performing MD simulation for one of the DNA demethylase enzymes using Amber. I have been able to generate both the "mol2" and "frcmod" files for the non-standard residues using...
09 September 2018 1,305 4 View
I optimized the structure of protein through energy minimization in a spherical water box with 0.15 M NaCl to maintain the charge at neutral using the CHARMM 27 force field, Langevin force field...
08 August 2018 7,303 5 View
I am trying to do metadynamics simulation for my protein. Can someone explain what is a collective variable, and on what basis we decide collective variables in a metadynamics run? Thanks.
08 August 2018 5,970 4 View
Dear community members, We have available WGBS data for a species. We used Bismark to map the reads to the reference genome. Unmethylated lambda phage DNA was spiked-in, to estimate the bisulfite...
19 July 2018 4,378 2 View
I have developed a set of hypotheses using shrodinger's Phase algorithm. One of the values returned for each hypothesis is 1%EF. What does this value mean and how do I interpret it? The other...
07 July 2018 7,083 0 View
Can anyone provide me the parameters of zinc oxide nanoparticle to carry out Gromacs Molecular Dynamics simulations? Thank you
07 July 2018 9,787 8 View
we do the research about the ion permeability for a protein channel.In previous studies (such as the POT ions), the ions didn't undergo a deep negative energy, the barrier is about 40-50...
07 July 2018 903 0 View
I am searching for software which use 100000 compounds for docking virtual screening and freely available. Please suggest me fast and reliable software's. Thank you.
07 July 2018 9,665 9 View
07 July 2018 1,646 4 View
I've been applying shock to a 3D cardiac model, but I want to change the algorithm that accounts for the ionic source term. How are the CHASTE cardiac downloadable CellML and .out files for the...
06 June 2018 6,574 2 View
Good day everyone! I am interested in learning molecular simulations of bio-molecules especially bacterial proteins. I have tried to watch/read a few lectures/articles regarding this. However, I...
06 June 2018 6,285 2 View
Hi, We were carrying out in vacuo energy minimization studies of a protein dimer (which is experimentally proven to be a dimer). Earlier, the same work has been done in our lab using an older...
05 May 2018 3,548 1 View
Hi there!! I want to do quality check some Sanger sequence reads and realized that the reads contain some odd letters (N, K, Y, B etc) different from the normal 4 DNA base letters (ATGC). What...
05 May 2018 5,497 6 View
I am trying to run a QM/MM MD calculation on an enzyme substrate system using AMBER after successful completion of MD production run in an Isobaric-Isothermal (NPT) ensemble without errors. I am...
05 May 2018 6,833 4 View
04 May 2018 3,562 3 View
We perform MD simulations with Amber on a protein dimer in different circumstances. In implicit solvent on 350 K the dimer dissociates after 2 ns, while in water box, NPT run it is still stable...
17 April 2018 1,540 3 View
Dear all, I have performed MD simulation for different carbon nanotubes (CNTs) in water using NAMD software. Each CNT is solvated in a water box initially and MD is performed for each box. Is...
10 April 2018 5,380 7 View
Hello Researcher, As one of my known Professor is looking for a Bioinformatics (Student/Researcher/Prof/etc) who can work with a team of collaborators for good publications and some funded...
04 April 2018 7,688 4 View
A genotype data for Genome Wide Association Analysis (GWAS) is provided as 0, 1, and 2 format where individuals along the row and each column is a SNP. The minor allele frequency (MAF) is...
04 April 2018 9,751 3 View
04 April 2018 1,022 3 View
04 April 2018 5,123 8 View
I am looking for any in silico tools that I can use to find mutated exons in a specific gene causing a genetic disorder. I can find mutations (in uniprot) but I am unable to find the exons.
03 March 2018 9,222 3 View
I was trying to simulate a 512-DPPC membrane after developing it from Tieleman's model of 128-DPPC bilayer. I removed the initial periodicity and the water molecules using trjconv as suggested by...
03 March 2018 4,949 8 View
I am reporting some cross-phenotype genetic correlations (LDSC method) that are statistically significant after multiple test correction. Peer reviewers have asked us to report top SNPs that might...
01 January 2018 3,167 4 View