StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions

Frontiers in Molecular Biosciences

Lin Li²  Chitra B. Karki²  Yixin Xie²  Weihong Qiu³  Yuejiao Xian⁴  Sebastian Miki Silva⁶ 

[1] Biophysics, Oregon State University, Corvallis, OR, United States;Computational Science Program, University of Texas at El Paso, El Paso, TX, United States;;Department of Biochemistry &Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, United States;Department of Physics, Oregon State University, Corvallis, OR, United States;Department of Physics, University of Texas at El Paso, El Paso, TX, United States;

关键词: protein-protein interactions;    protein-RNA/DNA interactions;    electrostatic force;    viral capsid assembly;    molecular motor;    kinesin;   

DOI  :  10.3389/fmolb.2020.627087

来源: DOAJ

【 摘 要 】

Studying biomolecular interactions is a crucial but challenging task. Due to their large scales, many biomolecular interactions are difficult to be simulated via all atom models. An effective approach to investigate the biomolecular interactions is highly demanded in many areas. Here we introduce a Structure Manipulation (StructureMan) program to operate the structures when studying the large-scale biomolecular interactions. This novel StructureMan tool provides comprehensive operations which can be utilized to study the interactions in various large biological systems. Combining with electrostatic calculation programs such as DelPhi and DelPhiForce, StructureMan was implemented to reveal the detailed electrostatic features in two large biological examples, the viral capsid and molecular motor-microtubule complexes. Applications on these two examples revealed interesting binding mechanisms in the viral capsid and molecular motor. Such applications demonstrated that the StructureMan can be widely used when studying the biomolecular interactions in large scale biological problems. This novel tool provides an alternative approach to efficiently study the biomolecular interactions, especially for large scale biology systems. The StructureMan tool is available at our website: http://compbio.utep.edu/static/downloads/script-for-munipulation2.zip.

【 授权许可】

Unknown