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ORCIDNathan A. Baker
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Journal Articles
- 2020
[j20]Francesca Grogan, Huan Lei, Xiantao Li, Nathan A. Baker
:
Data-driven molecular modeling with the generalized Langevin equation. J. Comput. Phys. 418: 109633 (2020)- 2017
- [j19]Lisa E. Felberg, David H. Brookes, Eng-Hui Yap, Elizabeth Jurrus, Nathan A. Baker, Teresa Head-Gordon:
PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. J. Comput. Chem. 38(15): 1275-1282 (2017) - 2016
- [j18]Xiu Yang, Huan Lei, Nathan A. Baker, Guang Lin:
Enhancing sparsity of Hermite polynomial expansions by iterative rotations. J. Comput. Phys. 307: 94-109 (2016) - 2015
- [j17]Huan Lei, Xiu Yang, Bin Zheng, Guang Lin, Nathan A. Baker:
Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation. Multiscale Model. Simul. 13(4): 1327-1353 (2015) - 2013
- [j16]Dennis G. Thomas, Jaehun Chun, Zhan Chen, Guowei Wei, Nathan A. Baker:
Parameterization of a geometric flow implicit solvation model. J. Comput. Chem. 34(8): 687-695 (2013) - 2012
- [j15]Victor Maojo, Martin Fritts, Fernando Martín-Sánchez, Diana de la Iglesia, Raul E. Cachau, Miguel García-Remesal, José Crespo, Joyce A. Mitchell, Alberto Anguita, Nathan A. Baker, José María Barreiro, Sonia E. Benitez, Guillermo de la Calle, Julio C. Facelli, Peter Ghazal, Antoine Geissbühler, Fernando D. González Nilo, Norbert M. Graf, Pierre Grangeat, Isabel Hermosilla, Rada Hussein, Josipa Kern, Sabine Koch, Yannick Legré, Victoria López-Alonso, Guillermo López-Campos, Luciano Milanesi, Vassilis Moustakis, Cristian R. Munteanu, Paula Otero, Alejandro Pazos, David Pérez-Rey, George Potamias, Ferran Sanz, Casimir A. Kulikowski:
Nanoinformatics: developing new computing applications for nanomedicine. Computing 94(6): 521-539 (2012) - 2011
- [j14]Dennis G. Thomas, Rohit V. Pappu, Nathan A. Baker:
NanoParticle Ontology for cancer nanotechnology research. J. Biomed. Informatics 44(1): 59-74 (2011) - [j13]Samir Unni, Yong Huang, Robert M. Hanson, Malcolm Tobias, Sriram Krishnan, Wilfred W. Li, Jens Erik Nielsen, Nathan A. Baker:
Web servers and services for electrostatics calculations with APBS and PDB2PQR. J. Comput. Chem. 32(7): 1488-1491 (2011) - 2010
- [j12]Zhan Chen, Nathan A. Baker, G. W. Wei:
Differential geometry based solvation model I: Eulerian formulation. J. Comput. Phys. 229(22): 8231-8258 (2010) - 2007
- [j11]Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens Erik Nielsen, Jan H. Jensen, Gerhard Klebe, Nathan A. Baker:
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35(Web-Server-Issue): 522-525 (2007) - 2006
- [j10]Xiaoyu Zhang, Chandrajit L. Bajaj, Bong June Kwon, Todd J. Dolinsky, Jens Erik Nielsen, Nathan A. Baker:
Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity. Multiscale Model. Simul. 5(4): 1196-1213 (2006) - 2005
- [j9]Jason Wagoner, Nathan A. Baker:
Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, " by Jason Wagoner and Nathan A. Baker. J. Comput. Chem. 26(8): 863- (2005) - 2004
- [j8]Todd J. Dolinsky, P. M. J. Burgers, Kevin Karplus, Nathan A. Baker:
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinform. 20(14): 2312-2314 (2004) - [j7]Jason Wagoner, Nathan A. Baker:
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. J. Comput. Chem. 25(13): 1623-1629 (2004) - [j6]Jason Wagoner, Nathan A. Baker:
Jason Wagoner and Nathan A. Baker, "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, "Journal of Computational Chemistry(2004) 25(13) 1623-1629. J. Comput. Chem. 25(14): 1801 (2004) - [j5]Todd J. Dolinsky, Jens Erik Nielsen, James Andrew McCammon, Nathan A. Baker:
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32(Web-Server-Issue): 665-667 (2004) - 2001
- [j4]Nathan A. Baker, David Sept, Michael J. Holst, James Andrew McCammon:
The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. IBM J. Res. Dev. 45(3): 427-438 (2001) - [j3]Michael J. Holst, Nathan A. Baker, Feng Wang:
ErratumAdaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. J. Comput. Chem. 22(4): 475 (2001) - 2000
- [j2]Michael J. Holst, Nathan A. Baker, Feng Wang:
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. J. Comput. Chem. 21(15): 1319-1342 (2000) - [j1]Michael J. Holst, Nathan A. Baker, Feng Wang:
Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. J. Comput. Chem. 21(15): 1343-1352 (2000)
Conference and Workshop Papers
- 2022
- [c7]Samuel Alexander Stein, Nathan Wiebe, Yufei Ding, Bo Peng, Karol Kowalski, Nathan A. Baker, James A. Ang, Ang Li:
EQC: ensembled quantum computing for variational quantum algorithms. ISCA 2022: 59-71 - 2020
- [c6]Arun V. Sathanur, Nathan A. Baker:
A clustering-based biased Monte Carlo approach to protein titration curve prediction. ICMLA 2020: 179-184 - 2018
- [c5]Garrett B. Goh, Charles Siegel, Abhinav Vishnu, Nathan O. Hodas, Nathan A. Baker:
How Much Chemistry Does a Deep Neural Network Need to Know to Make Accurate Predictions? WACV 2018: 1340-1349 - 2013
- [c4]Nathan A. Baker, Jonathan L. Barr, George T. Bonheyo, Cliff A. Joslyn, Kannan Krishnaswami, Mark E. Oxley, Rich Quadrel, Landon H. Sego, Mark F. Tardiff, Adam S. Wynne:
Research towards a systematic signature discovery process. ISI 2013: 301-308 - 2012
- [c3]Dennis G. Thomas, Satish Chikkagoudar, Alan R. Chappell, Nathan A. Baker:
Annotating the structure and components of a nanoparticle formulation using computable string expressions. BIBM Workshops 2012: 889-894 - [c2]Ferosh Jacob, Jeff Gray, Adam Wynne, Yan Liu, Nathan A. Baker:
Domain-specific languages for composing signature discovery workflows. DSM@SPLASH 2012: 61-64 - 2011
- [c1]K. S. M. Tozammel Hossain, Chris Bailey-Kellogg, Alan M. Friedman, Michael J. Bradley, Nathan A. Baker, Naren Ramakrishnan:
Using physicochemical properties of amino acids to induce graphical models of residue couplings. BIOKDD 2011: 3:1-3:10
Parts in Books or Collections
- 2004
- [p1]Nathan A. Baker:
Poisson-Boltzmann Methods for Biomolecular Electrostatics. Numerical Computer Methods, Part D 2004: 94-118
Informal and Other Publications
- 2019
- [i4]Guang Hao Low, Nicholas P. Bauman, Christopher E. Granade, Bo Peng, Nathan Wiebe, Eric J. Bylaska, Dave Wecker, Sriram Krishnamoorthy, Martin Roetteler, Karol Kowalski, Matthias Troyer, Nathan A. Baker:
Q# and NWChem: Tools for Scalable Quantum Chemistry on Quantum Computers. CoRR abs/1904.01131 (2019) - 2017
- [i3]Garrett B. Goh, Charles Siegel, Abhinav Vishnu, Nathan Oken Hodas, Nathan A. Baker:
Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models. CoRR abs/1706.06689 (2017) - [i2]Garrett B. Goh, Charles Siegel, Abhinav Vishnu, Nathan O. Hodas, Nathan A. Baker:
How Much Chemistry Does a Deep Neural Network Need to Know to Make Accurate Predictions? CoRR abs/1710.02238 (2017) - 2016
- [i1]Huan Lei, Nathan A. Baker, Xiantao Li:
Data-driven parameterization of the generalized Langevin equation. CoRR abs/1606.02596 (2016)
Coauthor Index
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