A New Graph Algorithm for the Analysis of Conformational Dynamics of Molecules

摘要

In molecular dynamics, there can be conformational dynamics of molecules. To identify the conformational space, chemists take a serie of snapshots of molecule at regular time then they try to analyze them by their eyes. When a serie contains thousands of snapshots or when the molecule is very big, this work is not possible. We present a new algorithm which aims to analyze the evolution of molecules under specific environmental conditions and characterize and quantify the isomers (conformations that could take a molecule). The algorithm is based on graph theory, it uses the distance geometry and some chemical properties (covalent bonds, H-bonds, proton transfer...). Optimizations were done to the algorithm to let it faster an efficient and to have a good time complexity. It can handle series with thousands of snapshots of molecules in Gas phase and analyze them in a few milliseconds.