J
Jens Erik Nielsen
Researcher at University College Dublin
Publications - 57
Citations - 11938
Jens Erik Nielsen is an academic researcher from University College Dublin. The author has contributed to research in topics: Active site & Protein pKa calculations. The author has an hindex of 34, co-authored 57 publications receiving 10352 citations. Previous affiliations of Jens Erik Nielsen include University of California, San Diego & University of British Columbia.
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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.
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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.
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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
TL;DR: The present energy function uses a minimum of computational resources and can therefore easily be used in protein design algorithms, and in the field of protein structure and folding pathways prediction where one requires a fast and accurate energy function.
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.
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Prolyl hydroxylase-1 negatively regulates IκB kinase-β, giving insight into hypoxia-induced NFκB activity
Eoin P. Cummins,Edurne Berra,Katrina M. Comerford,Amandine Ginouvès,Kathleen T. Fitzgerald,Fergal Seeballuck,Catherine Godson,Jens Erik Nielsen,Paul N. Moynagh,Jacques Pouysségur,Cormac T. Taylor +10 more
TL;DR: It is hypothesized that hypoxia releases repression of NFκB activity through decreased PHD-dependent hydroxylation of IKKβ, an event that may contribute to tumor development and progression through amplification of tumorigenic signaling pathways.