Rohit Shukla

Jaypee University of Information Technology | JUIT, J. P. University of Information Technology · Department of Biotechnology and Bioinformatics

Dear Researcher,

I am working in a machine learning project. I have just started from scratch and very beginner in this field. I want some suggestions to select the negative data-set for my Project.

I want to develop a tool which can identify the disease based on the sequence information. I have downloaded 600 annotated protein sequences (Positive data-set) from various databases which belongs from the diverse protein families and do not share a common domain. And I have selected the Negative data-set from the humans which are not identical (>50%) to the positive sequence. When I run the job using SVM, random forest, ANN etc. so it gives only 60% identity which is not good enough to make a good model. After that I have changed the negative data-set many times but the result was same. Then I have selected the negative data set from the plant and the accuracy is increased (>80%). So I have following doubts please clear that:

Dear researcher,

I want to simulate my protein with the denaturants (MW-139 Da). I am using Gromacs 2018.2 version and the extra molecules were added by using gmx insert-molecule command.

I want to add different concentration of denaturants like 10, 20............. til 90%. I have successfully added the 20% denaturants in the simulation box and run the simulation while I want to add more than 20% so the command adds a particular number and terminate with a massage (2241 is successfully added out of 3271 requested).

I have increased the box size so the number of denaturants were also increased due to increase of water molecules, so problem is same. I also read the gromacs mailing list but i can not find any solution.

Please suggest me how i can add the total molecules in the simulation box.

Thanks for your response in advance.

Dear researcher,

I want to find the Alzheimer paitient data in .bed file format for SNP related study. Several gene expression data are available in various databases but i can not find the link of the data which present in .bed file format.

Please suggest me some database or research articles.

Dear researcher,

I want to simulate my protein in different concentrations of Guanidinium chloride. I successfully added 4M GdnHCl in a cubic box. But when i want to neutrilize the system with the addition of 3915 chloride ions then it gave following error.

Fatal error:

Too many LINCS warnings (1030)

If you know what you are doing you can adjust the lincs warning threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,

but normally it is better to fix the problem

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

please suggest me that how i can solve my problem.

Dear researcher,

I want to simulate a protein-DNA complex. I can simulate the whole DNA but i want to simulate the nicked DNA. When i try to generate the topology of that ligand complex using GROMOS force field, it is giving the error.

Residue 'DC' not found in residue topology database

How can i solve this problem. please suggest me.

Dear researcher,

I want to simulate a selenium containing enzyme. But when i processed the selenium containing enzyme using pdb2gmx command so it is showing an error.

"Atom SE46 in residue CYS 597 was not found in rtp entry CYS with 11 atoms while sorting atoms"

please give me any suggestion how i can add the selenium during MDS.

Dear researcher,

                            I want to generate a free energy landscape using Essential dynamics analysis. I calculated a free energy landscape using g_sham tool. But it is not giving the idea about the minimized structure.

So my question is

1- How to predict a least energy confirmation of protein for docking using MDS

2- I attach a figure and i want to generate this type of figure

please provide me a solution. 

Thanks in advance.

Dear researcher,

                           I want to dock a small protein in the interface of diamer protein. When i submit the diamer structure in to HADDDOCK server it terminates the jobs and do not produce the result. But when i delete the one chain of diamer and proceed the docking it accept and produce the result.

So question is:

is there any problem in diamer construction. If yes please suggest me how to create the diamer.

is there any problem in docking then how can i resolve it.