This is an extended version of the Nonlinear Normal Modes Analysis extension, which computes the nonlinear normal modes of a molecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin [1].

Nonlinear Normal Modes Analysis

The user indicates the desired number of modes, the interactions cutoff distance and the potential function. In the output, each mode is represented by a slider. The user can visualize the motion of each mode independently by moving its corresponding slider manually or by checking its checkbox and then pressing on the play button. Also, the user can visualize the motion of a combination of modes selecting them before playing the motion. The transformations used in this motion can be set to linear or nonlinear and the amplitude of the motion can be increased/decreased by changing the scaling factor. During this motion, the user can activate a real time minimization using one of the provided algorithms (steepest descent, conjugated gradient or LBGFS) and defined values of minimization steps and minimization tolerance. The user can either save/export a given conformation of the structure or the entire displayed trajectory by going into the "Save Frames" tabulation of the SAMSON element.

Opening and closing binding pockets

In addition, the user can define a binding pocket and ask for a combination of modes that contribute the most to the opening and closing of this pocket. Please refer to this tutorial for more information.

References

[1] J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197

0.7.0: New functionality to compute a path between two protein structures. Step 1: Compute the normal modes of structure A. Step 2: Select structure B and, in the Structure definition tab of the app, click Define target. Step 3: Press the play button.;