A New Graph Algorithm for the Analysis of Conformational Dynamics of Molecules.
Lecture Notes in Electrical Engineering(2016)
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 orwhen 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.
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关键词
Good Time Complexity, Proton Transfer, Conformation, Reference Snapshot, Consecutive Snapshots
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