The Gauss machine-a DSP processor with a high RNS content. - Fred J. Taylor; Glenn S. Zelniker; Jeremy C. Smith; Jon Mellott (ICASSP, 1991)

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics. - Jérôme Baudry; Serge Crouzy; Benoît Roux; Jeremy C. Smith (J. Chem. Inf. Comput. Sci., 1997)

Fluctuation and Correlation in Crystalline Lysozyme. - Stéphanie Héry; Daniel Genest; Jeremy C. Smith (J. Chem. Inf. Comput. Sci., 1997)

Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13C14 and C15N16 bonds in the retinal of bacteriorhodopsin. - Serge Crouzy; Jérôme Baudry; Jeremy C. Smith; Benoît Roux (J. Comput. Chem., 1999)

An anti-snapback circuit technique for inhibiting parasitic bipolar conduction during EOS/ESD events. - Jeremy C. Smith (Microelectron. Reliab., 2001)

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?. - Sonja M. Schwarzl; Thomas B. Tschopp; Jeremy C. Smith; Stefan Fischer 004 (J. Comput. Chem., 2002)

How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin. - Sonja M. Schwarzl; Danzhi Huang; Jeremy C. Smith; Stefan Fischer 004 (Silico Biol., 2003)

Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. - Andrea C. Vaiana; Andreas Schulz; Jürgen Wolfrum; Markus Sauer; Jeremy C. Smith (J. Comput. Chem., 2003)

AFMM: A molecular mechanics force field vibrational parametrization program. - Andrea C. Vaiana; Zoe Cournia; Ion Bogdan Costescu; Jeremy C. Smith (Comput. Phys. Commun., 2005)

A molecular mechanics force field for biologically important sterols. - Zoe Cournia; Jeremy C. Smith; G. Matthias Ullmann (J. Comput. Chem., 2005)

Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins. - Sonja M. Schwarzl; Danzhi Huang; Jeremy C. Smith; Stefan Fischer 004 (J. Comput. Chem., 2005)

High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. - Franci Merzel; Jeremy C. Smith (J. Chem. Inf. Model., 2005)

A MOSFET power supply clamp with feedback enhanced triggering for ESD protection in advanced CMOS technologies. - Jeremy C. Smith; Gianluca Boselli (Microelectron. Reliab., 2005)

Clustering Analysis of Competitive Learning Network for Molecular Data. - Lin Wang 006; Minghu Jiang; Yinghua Lu; Frank Noé; Jeremy C. Smith (ISNN (1), 2006)

Self-Organizing Map Clustering Analysis for Molecular Data. - Lin Wang 006; Minghu Jiang; Yinghua Lu; Frank Noé; Jeremy C. Smith (ISNN (1), 2006)

Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the AlphaL leftrightharpoons Beta leftrightharpoons AlphaR Transitions in Octaalanine. - Frank Noé; Marcus Oswald; Gerhard Reinelt; Stefan Fischer 004; Jeremy C. Smith (Multiscale Model. Simul., 2006)

Coarse-grained force field for the nucleosome from self-consistent multiscaling. - Karine Voltz; Joanna Trylska; Valentina Tozzini; Vandana Kurkal-Siebert; Jörg Langowski; Jeremy C. Smith (J. Comput. Chem., 2008)

REACH: A program for coarse-grained biomolecular simulation. - Kei Moritsugu; Jeremy C. Smith (Comput. Phys. Commun., 2009)

A molecular mechanics force field for lignin. - Loukas Petridis; Jeremy C. Smith (J. Comput. Chem., 2009)

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. - Isabella Daidone; Hannes Neuweiler; Sören Doose; Markus Sauer; Jeremy C. Smith (PLoS Comput. Biol., 2010)

Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. - Barbara Collignon; Roland Schulz; Jeremy C. Smith; Jérôme Baudry (J. Comput. Chem., 2011)

Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes. - Jan-Hendrik Prinz; Martin Held; Jeremy C. Smith; Frank Noé (Multiscale Model. Simul., 2011)

Role of Histone Tails in Structural Stability of the Nucleosome. - Mithun Biswas; Karine Voltz; Jeremy C. Smith; Jörg Langowski (PLoS Comput. Biol., 2011)

Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations. - Lipi Thukral; Isabella Daidone; Jeremy C. Smith (PLoS Comput. Biol., 2011)

Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers. - Benjamin Lindner; Jeremy C. Smith (Comput. Phys. Commun., 2012)

Stereoselection in the diels-alderase ribozyme: A molecular dynamics study. - Tomasz Berezniak; Andres Jäschke; Jeremy C. Smith; Petra Imhof (J. Comput. Chem., 2012)

Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. - René Pool; Jaap Heringa; Martin Hoefling; Roland Schulz; Jeremy C. Smith; K. Anton Feenstra (J. Comput. Chem., 2012)

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. - Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R. Shirts; Jeremy C. Smith; Peter M. Kasson; David van der Spoel; Berk Hess; Erik Lindahl (Bioinform., 2013)

VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers. - Sally R. Ellingson; Jeremy C. Smith; Jérôme Baudry (J. Comput. Chem., 2013)

Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase. - Qi Chen; John K. Buolamwini; Jeremy C. Smith; Aixiu Li; Qin Xu; Xiaolin Cheng; Dongqing Wei (J. Chem. Inf. Model., 2013)

Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer. - Sally R. Ellingson; Dakshanamurthy Sivanesan; Milton Brown; Jeremy C. Smith; Jérôme Baudry (Concurr. Comput. Pract. Exp., 2014)

Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. - Christopher M. Topham; Jeremy C. Smith (Comput. Biol. Chem., 2015)

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. - Demian Riccardi; Jerry M. Parks; Alexander Johs; Jeremy C. Smith (J. Chem. Inf. Model., 2015)

Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions. - John R. Ossyra; Ada Sedova; Matthew B. Baker; Jeremy C. Smith (ISC Workshops, 2019)

Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer. - John R. Ossyra; Ada Sedova; Arnold N. Tharrington; Frank Noé; Cecilia Clementi; Jeremy C. Smith (ISC Workshops, 2019)

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. - Scott LeGrand; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Josh Vincent Vermaas; Rupesh Agarwal; Jeff Larkin; Duncan Poole; Diogo Santos-Martins; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; et al. (BCB, 2020)

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. - Hyea Hwang; Anthony Hazel; Peng Lian; Jeremy C. Smith; James C. Gumbart; Jerry M. Parks (J. Comput. Chem., 2020)

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. - Peng Lian; Luanjing Guo; Deepa Devarajan; Jerry M. Parks; Scott L. Painter; Scott C. Brooks; Jeremy C. Smith (J. Comput. Chem., 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - Atanu Acharya; Rupesh Agarwal; Matthew B. Baker; Jérôme Baudry; Debsindhu Bhowmik; Swen Böhm; Kendall G. Byler; Sam Yen-Chi Chen; Leighton Coates; Connor J. Cooper; Omar Demerdash; Isabella Daidone; et al. (J. Chem. Inf. Model., 2020)

Supercomputing Pipelines Search for Therapeutics Against COVID-19. - Josh Vincent Vermaas; Ada Sedova; Matthew B. Baker; Swen Boehm; David M. Rogers 001; Jeff Larkin; Jens Glaser; Micholas Dean Smith; Oscar R. Hernandez; Jeremy C. Smith (Comput. Sci. Eng., 2021)

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. - Christopher M. Topham; Jeremy C. Smith (J. Comput. Aided Mol. Des., 2021)

Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho. - Shih-Hsien Liu; Zhousheng Xiao; Sambit K. Mishra; Julie C. Mitchell; Jeremy C. Smith; L. Darryl Quarles; Loukas Petridis (J. Chem. Inf. Model., 2022)

HLA-Clus: HLA class I clustering based on 3D structure. - Yue Shen; Jerry M. Parks; Jeremy C. Smith (BMC Bioinform., 2023)

Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. - Rupesh Agarwal; Rajitha Rajeshwar T.; Jeremy C. Smith (J. Chem. Inf. Model., 2023)

Deep Learning Approaches for Predicting the Surface Tension of Ionic Liquids. - Nikhitha Gugulothu; Mood Mohan; Madaline R. Marland; Jeremy C. Smith; Michelle K. Kidder (J. Chem. Inf. Model., 2025)

Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools. - Yudan Shi; Jerry M. Parks; Jeremy C. Smith (J. Chem. Inf. Model., 2025)