MAS 2012 Proceeding

eSBMTools: python tools for enriched structure based modeling

Authors:   Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, Alexander Schug


Biomolecular simulations provide a computational microscope to dynamically visualize biomolecular systems with atomic resolution. Given the advances in speed of computational resources, simulations can complement experiments and help understand the relationship of folding, structure, and function of proteins, structured RNA, or DNA. Structure-based models (SBM) provide a computationally inexpensive tool to study the folding and structural assembly of (macro)biomolecules. Their theoretical foundations are energy landscape theory and the principle of minimal frustration. Here, we present ESBMTools python tools that assist to setup and analyze structure-based simulations of proteins and nucleic acids, both at the C? and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added as enrichments. One example would be docking protein complexes out of the composing individual known proteins plus bioinformatically derived information of the inter-protein interface contacts.

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