Saugata Hazra

11 Questions 26 Answers 0 Followers

Questions related from Saugata Hazra

Is the any software for finding upstream and downstream sequence of a gene?

For cloning purpose when we design primers, we need to deal with the upstream and downstream sequence of the cDNA. could you please suggest a software which would be appropriate in doing that?

07 July 2016 9,349 7 View

How to incorporate amino acids in the excel sheet ?

Hi Everyone, We want to develop a sequence database of protein. In the excel, we want to incorporate one letter code of amino acids in individual cells of the database. This would be extremely...

05 May 2016 926 2 View

Can anyone suggest a program to read trajectory files of different formats?

Can anyone suggest a program which could read all the different trajectory files (eg., .xtc, .dcd, .mdcrd) coming from different MD Simulation program packages.

02 February 2016 8,050 4 View

How we could calculate the range of phi and psi angle between a monopeptide.

For example, attached file is representing a .pdb file containing a peptide between two glycine. How we could measure the range of phi and psi angles here. Thanks in advance for your help and...

02 February 2016 3,138 4 View

Which one of the following would be a suitable method to calculate the binding affinity/binding free energy of a protein ligand interaction?

In case of studying protein-ligand interaction theoretically people generally use three methods to determine binding free energy, a) MMPBSA-GBSA method, b) linear interaction energy (LIE) and c)...

03 March 2015 5,938 1 View

How to model a protein with multiple domains and no template covering more than one domain?

I'm trying to model a protein which has multiple domains and templates available covering small parts of the sequence. It is a 4500 aa protein and to moderately covering the sequence it needs 7...

12 December 2013 2,916 19 View

Double Conformation of amino acid residues in a PDB file while runing MD Simulation

I'm preparing a PDB to run a MD simulation in AMBER. I have noticed that some of the amino acid residues exist in double confirmation. Should I remove all the double confirmation before the...

07 July 2013 1,882 3 View

Can someone recommend a good theoretical method by which two mutant variants could be differentiated?

Stability of protein mutants: I'm trying to design thermostable variants of a protein. Is it possible to theoretically differentiate them without doing simulation? What would be the parameters I...

07 July 2013 4,816 5 View

Can anyone help me with a suitable method for computational study of the thermal stability of protein mutants?

I'm studying stability of certain enzymes with their mesophilic and thermophilic homologues using MD Simulation methods. Using the information obtained from the study I'm trying to design point...

06 June 2013 3,015 3 View

How to relate loop flexibility with enzyme catalysis?

I'm working with an enzyme where some of the loops are playing important roles in catalysis. How could I study the relation of loop flexibility with the re-activity (computationally)?

06 June 2013 3,265 6 View

I need help with my MMPBSA calculation

I am running a binding energy calculation (MM-PBSA) for protein-ligand complex using Amber11 and AmberTools 1.5. I am following a Ross Walker tutorial (Link:...

02 February 2013 3,486 0 View