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Questions related from Nikhil Maroli
Anyone familiar with MSM modeling using pyemma, msmbuilder or any other packges? i am facing hard time on picking the correct packages for this. There are lot of dependecy issues, is there anyone...
10 April 2023 4,770 1 View
I would like to assess few enzyme proteins among the organism to understand the difference in their actions. The structure was modelled using homology modeling and same enzyme having different...
27 May 2019 1,369 8 View
Dear Researchers, We synthesised a novel aptamer against a particular protein/peptide target. Its a ssDNA with 87 bp and we would like to submit it to any database such as NCBI. Can anyone tell me...
12 November 2018 3,070 1 View
Dear all, how to predict a molecule is a reversible or irreversible enzyme inhibitor using in silico analysis: We are having a group of compounds for screening against a particular enzyme. We...
11 July 2017 5,519 8 View
Dear all, Is there any tool or server to predict the ability of molecules to penetrate blood-brain barrier? EDIT : Apart from http://www.cbligand.org/BBB/
02 June 2017 1,403 8 View
What are the cell lines I can use it for the experimental studies related to Aquaporin-2 and Vasopressin receptor, which is found in renal cells of the human? I have seen in Wikipedia that HEK...
21 March 2017 6,311 2 View
In order to assess and conclude the convergence of a protein ligandsimulations its better to go with multiple conformations or multiplevelocity method?
02 February 2017 4,155 1 View
It shows error when we load the metal in Autodock,so is there any method or protocol to follow?
18 December 2015 3,379 4 View
Hi all, Im looking for cyclic peptide structure and i wanted to know how the dihedral angels matters in peptide structure and how to define it for cyclic structure. if anyone has any kind of...
29 September 2015 3,382 5 View
I want to connect amino acids in cyclic form .when i connect last and first terminals it is breaking during energy minimization .so anyone knows is there any tools or software or how to do it...
01 July 2015 7,262 1 View
Hi, I have done energy minimization for my particular structure using gromacs ,after energy minimization what i found is that in my structure one bond is broken, it's a cyclic peptide constitutes...
23 June 2015 5,712 10 View
Anyone knows how to construct cyclic peptide using amino acids? any softwares? Theoretical for MD study (3D)
03 June 2015 757 15 View
In picture given atom and atom type ,what type of naming is it and how i can make this sort of naming from my structure ,what is this A and B etc... I'm from a physics background and I am not...
02 June 2015 9,035 3 View
Is there any program to convert ssDNA sequences to possible three-dimensional conformation for MD simulations? Edit: It is an aptamer generated against specific target
01 January 1970 9,771 4 View
Dear researchers, Currently we are working on ssDNA aptamers against various diseases in humans. We would like to get supports from the NMR data through collabarations. drop a message if anyone...
01 January 1970 4,558 3 View
I would like to calculate the reaction kinetics using gaussian. The reactants are two molecules that form amide bond and resultant is polyamide. What would be the transition state in this reaction?
01 January 1970 8,895 3 View
Dear all, I am looking for HIV antibodies named 240D and 246D. The crystal structure or aa sequence for this is available in any forms?
01 January 1970 4,467 2 View
Dear all, I have a big structure (~2000 atoms) to use in amber which is non-standard for amber forcefield. I wanted to convert syble mol2 file to amber type which shows amber atom types. Any...
01 January 1970 3,078 3 View
