T
Todd J. Dolinsky
Researcher at Washington University in St. Louis
Publications - 6
Citations - 6211
Todd J. Dolinsky is an academic researcher from Washington University in St. Louis. The author has contributed to research in topics: Software suite & Solver. The author has an hindex of 6, co-authored 6 publications receiving 5105 citations.
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Journal ArticleDOI
PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
TL;DR: The PDB2PQR web service is intended to facilitate the setup and execution of Electrostatics calculations for both experts and non-experts and thereby broaden the accessibility to the biological community of continuum electrostatics analyses of biomolecular systems.
Journal ArticleDOI
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Todd J. Dolinsky,Paul Czodrowski,Hui Li,Jens Erik Nielsen,Jan H. Jensen,Gerhard Klebe,Nathan A. Baker +6 more
TL;DR: The significantly expanded PDB2PQR is reported that includes robust standalone command line support, improved pKa estimation via the PROPKA framework, ligand parameterization via PEOE_PB charge methodology, expanded set of force fields and easily incorporated user-defined parameters via XML input files, and improvement of atom addition and optimization code.
Journal ArticleDOI
Improvements to the APBS biomolecular solvation software suite
Elizabeth Jurrus,Dave Engel,Keith T. Star,Kyle E. Monson,Juan Brandi,Lisa E. Felberg,David H. Brookes,Leighton Wilson,Jiahui Chen,Karina Liles,Minju Chun,Peter Li,David W. Gohara,Todd J. Dolinsky,Robert Konecny,David Ryan Koes,Jens Erik Nielsen,Teresa Head-Gordon,Weihua Geng,Robert Krasny,Guo-Wei Wei,Michael Holst,J. Andrew McCammon,Nathan A. Baker +23 more
TL;DR: The Adaptive Poisson-Boltzmann Solver (APBS) as mentioned in this paper was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications.
Journal ArticleDOI
Improvements to the APBS biomolecular solvation software suite.
Elizabeth Jurrus,Dave Engel,Keith T. Star,Kyle E. Monson,Juan Brandi,Lisa E. Felberg,David H. Brookes,Leighton Wilson,Jiahui Chen,Karina Liles,Minju Chun,Peter Li,David W. Gohara,Todd J. Dolinsky,Robert Konecny,David Ryan Koes,Jens Erik Nielsen,Teresa Head-Gordon,Weihua Geng,Robert Krasny,Guo-Wei Wei,Michael Holst,J. Andrew McCammon,Nathan A. Baker +23 more
TL;DR: The Adaptive Poisson-Boltzmann Solver (APBS) as mentioned in this paper was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological and biomedical applications.
Journal ArticleDOI
Application of new multiresolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity
Xiaoyu Zhang,Chandrajit L. Bajaj,Bong June Kwon,Todd J. Dolinsky,Jens E. Nielsen,Nathan A. Baker +5 more
TL;DR: The MACT method discriminates between protein chains at a level comparable to the Carbo similarity index method; i.e., it is able to accurately cluster proteins into functionally-relevant groups which demonstrate strong dependence on ligand binding sites.