Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. - Michael J. Holst; Nathan A. Baker; Feng Wang (J. Comput. Chem., 2000)

Adaptive multilevel finite element solution of the Poisson-Boltzmann equation II. Refinement at solvent-accessible surfaces in biomolecular systems. - Michael J. Holst; Nathan A. Baker; Feng Wang (J. Comput. Chem., 2000)

The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers. - Nathan A. Baker; David Sept; Michael J. Holst; James Andrew McCammon (IBM J. Res. Dev., 2001)

ErratumAdaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. - Michael J. Holst; Nathan A. Baker; Feng Wang (J. Comput. Chem., 2001)

Poisson-Boltzmann Methods for Biomolecular Electrostatics. - Nathan A. Baker (Numerical Computer Methods, Part D, 2004)

SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome. - Todd J. Dolinsky; P. M. J. Burgers; Kevin Karplus; Nathan A. Baker (Bioinform., 2004)

Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. - Jason Wagoner; Nathan A. Baker (J. Comput. Chem., 2004)

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. - Jason Wagoner; Nathan A. Baker (J. Comput. Chem., 2004)

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. - Todd J. Dolinsky; Jens Erik Nielsen; James Andrew McCammon; Nathan A. Baker (Nucleic Acids Res., 2004)

Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, " by Jason Wagoner and Nathan A. Baker. - Jason Wagoner; Nathan A. Baker (J. Comput. Chem., 2005)

Application of New Multiresolution Methods for the Comparison of Biomolecular Electrostatic Properties in the Absence of Global Structural Similarity. - Xiaoyu Zhang 011; Chandrajit L. Bajaj; Bong June Kwon; Todd J. Dolinsky; Jens Erik Nielsen; Nathan A. Baker (Multiscale Model. Simul., 2006)

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 (Nucleic Acids Res., 2007)

Differential geometry based solvation model I: Eulerian formulation. - Zhan Chen; Nathan A. Baker; G. W. Wei (J. Comput. Phys., 2010)

Using physicochemical properties of amino acids to induce graphical models of residue couplings. - K. S. M. Tozammel Hossain; Chris Bailey-Kellogg; Alan M. Friedman; Michael J. Bradley; Nathan A. Baker; Naren Ramakrishnan (BIOKDD, 2011)

NanoParticle Ontology for cancer nanotechnology research. - Dennis G. Thomas; Rohit V. Pappu; Nathan A. Baker (J. Biomed. Informatics, 2011)

Web servers and services for electrostatics calculations with APBS and PDB2PQR. - Samir Unni; Yong Huang; Robert M. Hanson; Malcolm Tobias; Sriram Krishnan; Wilfred W. Li; Jens Erik Nielsen; Nathan A. Baker (J. Comput. Chem., 2011)

Annotating the structure and components of a nanoparticle formulation using computable string expressions. - Dennis G. Thomas; Satish Chikkagoudar; Alan R. Chappell; Nathan A. Baker (BIBM Workshops, 2012)

Domain-specific languages for composing signature discovery workflows. - Ferosh Jacob; Jeff Gray 001; Adam Wynne; Yan Liu 001; Nathan A. Baker (DSM@SPLASH, 2012)

Nanoinformatics: developing new computing applications for nanomedicine. - 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; et al. (Computing, 2012)

Research towards a systematic signature discovery process. - 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 (ISI, 2013)

Parameterization of a geometric flow implicit solvation model. - Dennis G. Thomas; Jaehun Chun; Zhan Chen; Guowei Wei 001; Nathan A. Baker (J. Comput. Chem., 2013)

Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation. - Huan Lei; Xiu Yang; Bin Zheng; Guang Lin 001; Nathan A. Baker (Multiscale Model. Simul., 2015)

Data-driven parameterization of the generalized Langevin equation. - Huan Lei; Nathan A. Baker; Xiantao Li (CoRR, 2016)

Enhancing sparsity of Hermite polynomial expansions by iterative rotations. - Xiu Yang; Huan Lei; Nathan A. Baker; Guang Lin 001 (J. Comput. Phys., 2016)

Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models. - Garrett B. Goh; Charles Siegel; Abhinav Vishnu; Nathan Oken Hodas; Nathan A. Baker (CoRR, 2017)

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. - Lisa E. Felberg; David H. Brookes; Eng-Hui Yap; Elizabeth Jurrus; Nathan A. Baker; Teresa Head-Gordon (J. Comput. Chem., 2017)

How Much Chemistry Does a Deep Neural Network Need to Know to Make Accurate Predictions? - Garrett B. Goh; Charles Siegel; Abhinav Vishnu; Nathan O. Hodas; Nathan A. Baker (WACV, 2018)

Q# and NWChem: Tools for Scalable Quantum Chemistry on Quantum Computers. - 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 (CoRR, 2019)

A clustering-based biased Monte Carlo approach to protein titration curve prediction. - Arun V. Sathanur; Nathan A. Baker (ICMLA, 2020)

Data-driven molecular modeling with the generalized Langevin equation. - Francesca Grogan; Huan Lei; Xiantao Li; Nathan A. Baker (J. Comput. Phys., 2020)

EQC: ensembled quantum computing for variational quantum algorithms. - Samuel Alexander Stein; Nathan Wiebe; Yufei Ding 001; Bo Peng; Karol Kowalski; Nathan A. Baker; James A. Ang; Ang Li 006 (ISCA, 2022)