| Attributs | Valeurs |
|---|
| type
| |
| Is Part Of
| |
| Subject
| |
| Title
| - Petri nets formalism facilitates analysis of complex biomolecular structural data
|
| Date
| |
| has manifestation of work
| |
| related by
| |
| Author
| |
| Abstract
| - Molecular dynamics (MD) simulation is a popular method of protein and nucleic acids research. Current MD output trajectories are huge files and therefore they are hard to analyze. Petri nets (PNs) is a mathematical modeling language that allows for concise, graphical representation of complex data. We have developed a few algorithms for PNs generation from such large MD trajectories. One of them, called the One Place One Conformation (OPOC) algorithm, is presented in a greater detail. In the OPOC algorithm one biomolecular conformation corresponds to one PN place and a transition occurring in PN graph is related to a change between biomolecules conformations. As case studies three simulations are analyzed: an enforced steered MD (SMD) dissociation of a transthyretin protein tetramer into dimers, the SMD dissociation of an antibody-antigen complex and a classical MD simulation of transthyretin. We show that PNs reproduce events hidden in MD trajectories and enable observations of the conformational space features hard-to-see by the other clustering methods. Thus, a fundamental process of biomolecular data classification may be optimized using the PN approach.
|
| article type
| |
| publisher identifier
| |
| Date Copyrighted
| |
| Rights
| - © EDP Sciences, ROADEF, SMAI 2016
|
| Rights Holder
| |
| is part of this journal
| |
| is primary topic
of | |
