Dr. Dror Tobi

GNM Align

A program to compare proteins’ dynamics by aligning GNM slow modes

gnm modes calculation:

GNM Web Server by Ivet Bahar’s group

GNM Stand alone program by Ivet Bahar’s group

Another GNM stand alone program used in this tutotial (written by us)

compilation:

tar -xvzf gnmcpp1.tar.gz

cd gnmcpp1

g++ -O2 gnm.cpp -o gnm

GNM Pairwise Alignment software

gnmalign stand alone program

compilation:

tar -xvzf galign.tar.gz

cd galign

make

Tutorials

GNM align Tutorial

Input files

References

  1. D.Tobi; Dynamics alignment: Comparison of protein dynamics in the SCOP database, Proteins 80(4):1167-76 (2012)
  2. D.Tobi; Large Scale Analysis of the Dynamics of Enzymes, Proteins 81(11):1910-8 (2013)