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Questions related from Mahendra B Thapa
A pdb file (biological assembly of a virus capid) has 24 model and each model has 3 chains A,B and C. I am interested to keep only those models which are in contact with chain A of model 1....
24 June 2016 5,966 3 View
Dear researchers, I use 'ModLoop server' to add coordinates of missing residues in a pdb file. I tried to use 'Swiss model server' for the same purpose but it didn't work by some reasons. If there...
26 January 2016 5,391 9 View
Dear Researchers, DNAbinder, DNABIND and HMMER are useful for web servers for predicting DNA-binding proteins and they take many sequences at a time. BindN, DR_bind, DNA Bind Prot, metaDBSite, and...
16 July 2015 8,418 3 View
Dear Researchers To find the sequence entropy of a protein (say, pdb code 4ICB) / DNA , I am using some codes written in C program. For this, I need to use BLAST and ClustalW2 , and resulting...
19 April 2015 3,151 8 View
Dear Researchers, I have a single pdb file with a large number of structures (say, 100000 in NMR style pdb). To cluster these pdb files, I used some some of the techniques based on google search...
03 January 2015 3,566 1 View
Dear Researchers, I am interested to measure the hinge motion around the hinge region of a protein and visualise the motion as well. By normal mode analysis and all-atom simulation, I generated...
30 September 2014 629 4 View
Dear Researchers, I am trying to simulate a protein that binds a complex ligand. Small equilibration step was ok but failed while trying to heat the system due to high values of vander waals...
26 September 2014 3,887 4 View
Dear Researchers, I have been using ModLoop web-server to add residues which are not given in pdb file of a protein; I mean to fill the gap in the pdb file. I am interested to use another loop...
16 August 2014 4,688 2 View
I've been using simple articles (such as "An Astronomer Looks at Astrology" by Andrew Fraknoi) or research papers as alternative assignments for my introductory astronomy course. Many of my...
01 January 1970 525 1 View
