Similarity-ordered heat maps: A new tool for analyzing molecular dynamics simulations

Authors

• P Cruz
• R Squires
• H Griggs
• A Gabrielian
• D Hurt

Abstract

​​Molecular dynamics (MD) simulations provide methods for studying the structures available to molecular systems and how they evolve over time. MD methods can provide insights on molecules for which no experimental structural data is available. One class of systems for which there is currently a paucity of experimental structures is bioactive peptides. The computing power of the NIAID high performance cluster was used in a program of high-throughput MD calculations to add 3D structural information to the online DBAASP peptide database.​ As an aid to analyzing peptide MD simulations, a new graphical method was developed, the Similarity-Ordered Heat Map. These heat maps utilize an internal-coordinate measure, the Cα torsion angle, which describes the structure of each simulation frame, provides a simplified means of comparing the structures of different frames, and identifies the representative frame that is most similar to all the other frames. A heat map is then constructed by ordering all frames according to their distance from the representative frame, and then building a square matrix that color-codes the distance of each frame from every other frame. Similarity-Ordered Heat Maps are particularly useful for providing at-a-glance information characterizing peptide (and other) MD simulations. Square blocks of similar color within the heat map indicate how many different major and minor structural motifs are represented in the simulation, the fraction of the simulation represented by each state, and how similar they are to each other. Examples representing several different types of simulation outcomes will be shown and discussed.​​

Scientific Focus Area: Structural Biology

This page was last updated on Friday, March 26, 2021