Contact experts in Bioinformatics and Computational Biology to get answers
1,096 views 2,327 posts
Questions related to Bioinformatics and Computational Biology
I have tried to predicted the 3D structure by using multiple online softwares like I-TASSAR, MUSTER, Swiss-Model and (PS)2 but predicted 3D structure from each software has bad quality and can not...
28 November 2018 9,145 3 View
11 November 2018 5,581 6 View
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...
15 September 2018 3,179 2 View
09 September 2018 1,173 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 7,141 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 5,739 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 4,195 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 6,949 0 View
Can anyone provide me the parameters of zinc oxide nanoparticle to carry out Gromacs Molecular Dynamics simulations? Thank you
07 July 2018 9,683 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 780 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 9,484 9 View
07 July 2018 1,535 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 6,456 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 6,126 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 3,326 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 5,402 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 6,679 4 View
04 May 2018 3,385 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 1,387 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 5,242 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 7,561 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 9,623 3 View
04 April 2018 908 3 View
04 April 2018 5,003 8 View