Show simple item record

dc.contributor.authorJo, Sunhwan
dc.contributor.authorVargyas, Miklos
dc.contributor.authorVasko-Szedlar, Judit
dc.contributor.authorRoux, Benoît
dc.contributor.authorIm, Wonpil
dc.date.accessioned2014-04-17T13:26:52Z
dc.date.available2014-04-17T13:26:52Z
dc.date.issued2008-05-07
dc.identifier.citationJo, Sunhwan, and Wonpil Im. 2013. “Glycan Fragment Database: A Database of PDB-Based Glycan 3D Structures.” Nucleic Acids Research 41 (D1): D470–D474. http://dx.doi.org/10.1093/nar/gks987
dc.identifier.urihttp://hdl.handle.net/1808/13531
dc.description.abstractPBEQ-Solver provides a web-based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann (PB) equations and interactively visualize the electrostatic potential. PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein–protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue. All the calculations can be performed in both aqueous solvent and membrane environments (with a cylindrical pore in the case of membrane). PBEQ-Solver uses the PBEQ module in the biomolecular simulation program CHARMM to solve the finite-difference PB equation of molecules specified by users. Users can interactively inspect the calculated electrostatic potential on the solvent-accessible surface as well as iso-electrostatic potential contours using a novel online visualization tool based on MarvinSpace molecular visualization software, a Java applet integrated within CHARMM-GUI (http://www.charmm-gui.org). To reduce the computational time on the server, and to increase the efficiency in visualization, all the PB calculations are performed with coarse grid spacing (1.5 Å before and 1 Å after focusing). PBEQ-Solver suggests various physical parameters for PB calculations and users can modify them if necessary. PBEQ-Solver is available at http://www.charmm-gui.org/input/pbeqsolver.
dc.description.sponsorshipSunhwan Jo is the recipient of the Undergraduate Research Assistant Fund from the University of Kansas. Wonpil Im is 2007 Alfred P. Sloan Research Fellow. This work was supported by institutional funding from the University of Kansas (to W.I.) and grant 0415784 from the National Science Foundation (to B.R.). Funding to pay the Open Access publication charges for this article was provided by National Science Foundation grant MCB-0415784.
dc.publisherOxford University Press
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by-nc/2.0/uk/
dc.titlePBEQ-Solver for online visualization of electrostatic potential of biomolecules
dc.typeArticle
kusw.kuauthorJo, Sunhwan
kusw.kuauthorIm, Wonpil
kusw.kudepartmentDepartment of Chemisty
kusw.kudepartmentDepartment of Molecular Biology
dc.identifier.doi10.1093/nar/gkn314
dc.identifier.orcidhttps://orcid.org/0000-0002-4104-6473
kusw.oaversionScholarly/refereed, publisher version
kusw.oapolicyThis item does not meet KU Open Access policy criteria.
dc.rights.accessrightsopenAccess


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.