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您的检索式：作者名="Maxim Zhenirovskyy"
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| 1 | DelEnsembleElec:Computing Ensemble-Averaged Electrostatics Using DelPhi显示文摘A new VMD plugin that interfaces with DelPhi to provide ensemble-averaged electrostatic calculations using the Poisson-Boltzmann equation is presented.The general theory and context of this approach are discussed,and examples of the plugin interface and calculations are presented.This new tool is applied to systems of current biological interest,obtaining the ensemble-averaged electrostatic properties of the two major influenza virus glycoproteins,hemagglutinin and neuraminidase,from explicitly solvated all-atom molecular dynamics trajectories.The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples,revealing how the plugin can be a powerful tool in facilitating the modeling of electrostatic interactions in biological systems. | Lane W.Votapka Luke Czapla Maxim Zhenirovskyy Rommie E.Amaro | 2013 | Communications in Computational Physics2013，13，1： | 0 |
| 2 | DelPhi Web Server:A Comprehensive Online Suite for Electrostatic Calculations of Biological Macromolecules and Their Complexes显示文摘Here we report a web server,the DelPhi web server,which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions,and dielectric map.The server provides extra services to fix structural defects,as missing atoms in the structural file and allows for generation of missing hydrogen atoms.The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22,Amber98 or OPLS.Upon completion of the calculations,the user is given option to download fixed and protonated structural file,together with the parameter and Delphi output files for further analysis.Utilizing Jmol viewer,the user can see the corresponding structural file,to manipulate it and to change the presentation.In addition,if the potential map is requested to be calculated,the potential can be mapped onto the molecule surface.The DelPhi web server is available from http://gffzzde59a5d64e5c401ehqk5pn0k6xcqk69ux.ffgz.tsg.suse.edu.cn/delphi webserver. | Subhra Sarkar Shawn Witham Jie Zhang Maxim Zhenirovskyy Walter Rocchia Emil Alexov | 2013 | Communications in Computational Physics2013，13，1： | 0 |
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