Rajeev Ranjan Roy

10 Questions 25 Answers 0 Followers

Questions related from Rajeev Ranjan Roy

Tools for modeling 3D structures of complex saccharides?

I want to model some complex polysaccharides containing non-conventional saccharides as building units. The structures should retain the proper glyscosidic linkage. Please suggest me some tools...

09 September 2016 1,312 11 View

What is the accurate definition of interactome, can we use the term in context of protein-ligand complex?

Can we use the term in context of a particular ligand interaction with the binding site residues of a particular protein, by generating numerous frames of a stable protein-ligand complex using...

04 April 2016 2,136 2 View

How to calculate diffusion rate of a molecule into the solvent using molecular dynamics simulation?

I want to calculate diffusion rate of a substrate computationally using molecular dynamics simulation, please help.

10 October 2015 2,389 1 View

Can we use the potential energy values generated after minimization of small molecules, to compare their stability?

Its well known fact, potential energy generated by molecular minimization usually used to check molecules stability and is the function of torsion energy, bend energy, bond stretch energy,...

06 June 2015 4,713 15 View

What's 'single-trajectory' simulation and how is it different from normal MD simulation?

Which is best for ligand-protein complex, binding affinity calculation?

06 June 2014 3,813 5 View

What is the basic step for doing Proteochemometrics modelling?

12 December 2013 1,932 1 View

Are there any bioinformatics tools which can identify the physicochemical properties of binding pocket of different protein?

I want to identify the physicochemical properties of binding pockets of different proteins, as it has reported in some literature that the binding pocket of each protein has different and unique...

11 November 2013 3,355 9 View

Could anyone give a suggestion regarding substitute for MD simulation for binding energy calculation of docked protein-ligand complexes?

I have done the docking by using DOCK6 software and on the basis of good poses and grid score sorted out a good docked ligand conformation. Now I want to calculate the accurate or some what close...

11 November 2013 2,936 3 View

How to differentiate among the mode of binding of ligands in different proteins having same set of identical or similar active site residues?

I am doing docking studies on some proteins belonging to same protein family but different organism, but don't know how to differentiate out the difference in binding mode of ligands to the...

11 November 2013 5,991 1 View

Which should be given more importance docked good poses or binding energies of docked ligands?

10 October 2013 8,542 20 View