Jeremy C. Smith

47 papers Misc 1Journal 41Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools. J. Chem. Inf. Model. Yudan Shi, Jerry M. Parks, Jeremy C. Smith
2025	J	`jnl`	Deep Learning Approaches for Predicting the Surface Tension of Ionic Liquids. J. Chem. Inf. Model. Nikhitha Gugulothu, Mood Mohan, Madaline R. Marland, Jeremy C. Smith, Michelle K. Kidder
2025	J	`jnl`	Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures. J. Chem. Inf. Model. Zhangmin Wan, Yan Yu, Gio Ferson M. Bautista, Simcha Srebnik, Jeremy C. Smith, Orlando J. Rojas
2023	J	`jnl`	Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J. Chem. Inf. Model. Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith
2023	J	`jnl`	HLA-Clus: HLA class I clustering based on 3D structure. BMC Bioinform. Yue Shen, Jerry M. Parks, Jeremy C. Smith
2022	J	`jnl`	Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho. J. Chem. Inf. Model. Shih-Hsien Liu, Zhousheng Xiao, Sambit K. Mishra, Julie C. Mitchell, Jeremy C. Smith, L. Darryl Quarles, Loukas Petridis
2021	J	`jnl`	Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J. Comput. Aided Mol. Des. Christopher M. Topham, Jeremy C. Smith
2021	J	`jnl`	Supercomputing Pipelines Search for Therapeutics Against COVID-19. Comput. Sci. Eng. Josh Vincent Vermaas, Ada Sedova, Matthew B. Baker, Swen Boehm, David M. Rogers, Jeff Larkin, Jens Glaser, Micholas Dean Smith, Oscar R. Hernandez, Jeremy C. Smith
2020	J	`jnl`	A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. J. Comput. Chem. Hyea Hwang, Anthony Hazel, Peng Lian, Jeremy C. Smith, James C. Gumbart, Jerry M. Parks
2020	—	`conf`	GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. BCB 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, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova
2020	J	`jnl`	Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 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, John D. Eblen, Sally R. Ellingson, Stefano Forli, Jens Glaser, James C. Gumbart, John Gunnels, Oscar R. Hernandez, Stephan Irle, Daniel W. Kneller, Andrey Kovalevsky, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu, Julie C. Mitchell, Gilchan Park, Jerry M. Parks, Anna Pavlova, Loukas Petridis, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova, Yue Shen, Jeremy C. Smith, Micholas Dean Smith, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas, Van Quan Vuong, Junqi Yin, Shinjae Yoo, Mai Zahran, Laura Zanetti Polzi
2020	J	`jnl`	The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. J. Comput. Chem. Peng Lian, Luanjing Guo, Deepa Devarajan, Jerry M. Parks, Scott L. Painter, Scott C. Brooks, Jeremy C. Smith
2019	—	`conf`	Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions. ISC Workshops John R. Ossyra, Ada Sedova, Matthew B. Baker, Jeremy C. Smith
2019	—	`conf`	Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer. ISC Workshops John R. Ossyra, Ada Sedova, Arnold N. Tharrington, Frank Noé, Cecilia Clementi, Jeremy C. Smith
2015	J	`jnl`	HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. J. Chem. Inf. Model. Demian Riccardi, Jerry M. Parks, Alexander Johs, Jeremy C. Smith
2015	J	`jnl`	Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Comput. Biol. Chem. Christopher M. Topham, Jeremy C. Smith
2014	J	`jnl`	Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer. Concurr. Comput. Pract. Exp. Sally R. Ellingson, Dakshanamurthy Sivanesan, Milton Brown, Jeremy C. Smith, Jérôme Baudry
2013	J	`jnl`	GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 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
2013	J	`jnl`	Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase. J. Chem. Inf. Model. Qi Chen, John K. Buolamwini, Jeremy C. Smith, Aixiu Li, Qin Xu, Xiaolin Cheng, Dongqing Wei
2013	J	`jnl`	VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers. J. Comput. Chem. Sally R. Ellingson, Jeremy C. Smith, Jérôme Baudry
2012	J	`jnl`	Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem. René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
2012	J	`jnl`	Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers. Comput. Phys. Commun. Benjamin Lindner, Jeremy C. Smith
2012	J	`jnl`	Stereoselection in the diels-alderase ribozyme: A molecular dynamics study. J. Comput. Chem. Tomasz Berezniak, Andres Jäschke, Jeremy C. Smith, Petra Imhof
2011	J	`jnl`	Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul. Jan-Hendrik Prinz, Martin Held, Jeremy C. Smith, Frank Noé
2011	J	`jnl`	Role of Histone Tails in Structural Stability of the Nucleosome. PLoS Comput. Biol. Mithun Biswas, Karine Voltz, Jeremy C. Smith, Jörg Langowski
2011	J	`jnl`	Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations. PLoS Comput. Biol. Lipi Thukral, Isabella Daidone, Jeremy C. Smith
2011	J	`jnl`	Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J. Comput. Chem. Barbara Collignon, Roland Schulz, Jeremy C. Smith, Jérôme Baudry
2010	J	`jnl`	Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. PLoS Comput. Biol. Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith
2009	J	`jnl`	A molecular mechanics force field for lignin. J. Comput. Chem. Loukas Petridis, Jeremy C. Smith
2009	J	`jnl`	REACH: A program for coarse-grained biomolecular simulation. Comput. Phys. Commun. Kei Moritsugu, Jeremy C. Smith
2008	J	`jnl`	Coarse-grained force field for the nucleosome from self-consistent multiscaling. J. Comput. Chem. Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy C. Smith
2006	—	`conf`	Clustering Analysis of Competitive Learning Network for Molecular Data. ISNN (1) Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith
2006	J	`jnl`	Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the Multiscale Model. Simul. Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith
2006	—	`conf`	Self-Organizing Map Clustering Analysis for Molecular Data. ISNN (1) Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith
2005	J	`jnl`	A MOSFET power supply clamp with feedback enhanced triggering for ESD protection in advanced CMOS technologies. Microelectron. Reliab. Jeremy C. Smith, Gianluca Boselli
2005	J	`jnl`	A molecular mechanics force field for biologically important sterols. J. Comput. Chem. Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann
2005	J	`jnl`	AFMM: A molecular mechanics force field vibrational parametrization program. Comput. Phys. Commun. Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith
2005	J	`jnl`	High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. J. Chem. Inf. Model. Franci Merzel, Jeremy C. Smith
2005	J	`jnl`	Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins. J. Comput. Chem. Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer
2003	J	`jnl`	How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin. Silico Biol. Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer
2003	J	`jnl`	Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J. Comput. Chem. Andrea C. Vaiana, Andreas Schulz, Jürgen Wolfrum, Markus Sauer, Jeremy C. Smith
2002	J	`jnl`	Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?. J. Comput. Chem. Sonja M. Schwarzl, Thomas B. Tschopp, Jeremy C. Smith, Stefan Fischer
2001	J	`jnl`	An anti-snapback circuit technique for inhibiting parasitic bipolar conduction during EOS/ESD events. Microelectron. Reliab. Jeremy C. Smith
1999	J	`jnl`	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. J. Comput. Chem. Serge Crouzy, Jérôme Baudry, Jeremy C. Smith, Benoît Roux
1997	J	`jnl`	Fluctuation and Correlation in Crystalline Lysozyme. J. Chem. Inf. Comput. Sci. Stéphanie Héry, Daniel Genest, Jeremy C. Smith
1997	J	`jnl`	Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics. J. Chem. Inf. Comput. Sci. Jérôme Baudry, Serge Crouzy, Benoît Roux, Jeremy C. Smith
1991	Misc	`conf`	The Gauss machine-a DSP processor with a high RNS content. ICASSP Fred J. Taylor, Glenn S. Zelniker, Jeremy C. Smith, Jon Mellott