[gmx-users] antigen-antibody insilico MD using GROMACS

Deep kumar deepak.choubey86 at gmail.com
Fri Feb 23 15:24:39 CET 2018

Hi Gromacs users,

I am studying antigen-antibody interaction at protein level. I have a
protein sequence (no crystal structure, length 180 residues) of the
antigen, and have predicted the secondary structure of it (and modeled). By
performing conserved domain search using inferno and NCBI I found out a
domain in the antigen - PCC1 (residue 90 to 160). I am interested to know
how the antigen interacts with the antibody (2000 residues) *in silico*.
The ultimate aim is to find out "how the antigen interacts with the
antibody, and predict the possible domains used by the antigen to interact
with the antibody". I would really appreciate your valuable suggestions on
how this can be done using GROMACS MD. Please let me know if I need to
provide any further information. Thanks for your time.


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