Jeremy C. Smith

Publication Activity (10 Years)

Years Active: 1991-2023
Publications (10 Years): 13

Top Topics

Design Solutions

Amino Acid Residues

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

Publications

Yue Shen, Jerry M. Parks, Jeremy C. Smith
HLA-Clus: HLA class I clustering based on 3D structure. BMC Bioinform. 24 (1) (2023)
Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith
Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J. Chem. Inf. Model. 63 (23) (2023)
Shih-Hsien Liu, Zhousheng Xiao, Sambit K. Mishra, Julie C. Mitchell, Jeremy C. Smith, L. Darryl Quarles, Loukas Petridis
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. 62 (15) (2022)
Christopher M. Topham, Jeremy C. Smith
Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J. Comput. Aided Mol. Des. 35 (3) (2021)
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
Supercomputing Pipelines Search for Therapeutics Against COVID-19. Comput. Sci. Eng. 23 (1) (2021)
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
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. BCB (2020)
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, D. W. Kneller, A. 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, Y. 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
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60 (12) (2020)
Peng Lian, Luanjing Guo, Deepa Devarajan, Jerry M. Parks, Scott L. Painter, Scott C. Brooks, Jeremy C. Smith
The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. J. Comput. Chem. 41 (2) (2020)
Hyea Hwang, Anthony Hazel, Peng Lian, Jeremy C. Smith, James C. Gumbart, Jerry M. Parks
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. J. Comput. Chem. 41 (6) (2020)
John R. Ossyra, Ada Sedova, Matthew B. Baker, Jeremy C. Smith
Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions. ISC Workshops (2019)
John R. Ossyra, Ada Sedova, Arnold N. Tharrington, Frank Noé, Cecilia Clementi, Jeremy C. Smith
Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer. ISC Workshops (2019)
Demian Riccardi, Jerry M. Parks, Alexander Johs, Jeremy C. Smith
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. J. Chem. Inf. Model. 55 (4) (2015)
Christopher M. Topham, Jeremy C. Smith
Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Comput. Biol. Chem. 54 (2015)
Sally R. Ellingson, Dakshanamurthy Sivanesan, Milton Brown, Jeremy C. Smith, Jérôme Baudry
Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer. Concurr. Comput. Pract. Exp. 26 (6) (2014)
Qi Chen, John K. Buolamwini, Jeremy C. Smith, Aixiu Li, Qin Xu, Xiaolin Cheng, Dongqing Wei
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase. J. Chem. Inf. Model. 53 (12) (2013)
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
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29 (7) (2013)
Sally R. Ellingson, Jeremy C. Smith, Jérôme Baudry
VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers. J. Comput. Chem. 34 (25) (2013)
Tomasz Berezniak, Andres Jäschke, Jeremy C. Smith, Petra Imhof
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study. J. Comput. Chem. 33 (19) (2012)
Benjamin Lindner, Jeremy C. Smith
Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers. Comput. Phys. Commun. 183 (7) (2012)
René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra
Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. J. Comput. Chem. 33 (12) (2012)
Jan-Hendrik Prinz, Martin Held, Jeremy C. Smith, Frank Noé
Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul. 9 (2) (2011)
Mithun Biswas, Karine Voltz, Jeremy C. Smith, Jörg Langowski
Role of Histone Tails in Structural Stability of the Nucleosome. PLoS Comput. Biol. 7 (12) (2011)
Barbara Collignon, Roland Schulz, Jeremy C. Smith, Jérôme Baudry
Task-parallel message passing interface implementation of Autodock4 for docking of very large databases of compounds using high-performance super-computers. J. Comput. Chem. 32 (6) (2011)
Lipi Thukral, Isabella Daidone, Jeremy C. Smith
Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations. PLoS Comput. Biol. 7 (9) (2011)
Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith
Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains. PLoS Comput. Biol. 6 (1) (2010)
Loukas Petridis, Jeremy C. Smith
A molecular mechanics force field for lignin. J. Comput. Chem. 30 (3) (2009)
Kei Moritsugu, Jeremy C. Smith
REACH: A program for coarse-grained biomolecular simulation. Comput. Phys. Commun. 180 (7) (2009)
Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy C. Smith
Coarse-grained force field for the nucleosome from self-consistent multiscaling. J. Comput. Chem. 29 (9) (2008)
Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith
Transitions in Octaalanine. Multiscale Model. Simul. 5 (2) (2006)
Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith
Clustering Analysis of Competitive Learning Network for Molecular Data. ISNN (1) (2006)
Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith
Self-Organizing Map Clustering Analysis for Molecular Data. ISNN (1) (2006)
Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer
Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins. J. Comput. Chem. 26 (13) (2005)
Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann
A molecular mechanics force field for biologically important sterols. J. Comput. Chem. 26 (13) (2005)
Franci Merzel, Jeremy C. Smith
High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. J. Chem. Inf. Model. 45 (6) (2005)
Jeremy C. Smith, Gianluca Boselli
A MOSFET power supply clamp with feedback enhanced triggering for ESD protection in advanced CMOS technologies. Microelectron. Reliab. 45 (2) (2005)
Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith
AFMM: A molecular mechanics force field vibrational parametrization program. Comput. Phys. Commun. 167 (1) (2005)
Andrea C. Vaiana, Andreas Schulz, Jürgen Wolfrum, Markus Sauer, Jeremy C. Smith
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. J. Comput. Chem. 24 (5) (2003)
Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer
How well does charge reparametrisation account for solvent screening in molecular mechanics calculations? The example of myosin. Silico Biol. 3 (1-2) (2003)
Sonja M. Schwarzl, Thomas B. Tschopp, Jeremy C. Smith, Stefan Fischer
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?. J. Comput. Chem. 23 (12) (2002)
Jeremy C. Smith
An anti-snapback circuit technique for inhibiting parasitic bipolar conduction during EOS/ESD events. Microelectron. Reliab. 41 (3) (2001)
Serge Crouzy, Jérôme Baudry, Jeremy C. Smith, Benoît Roux
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. 20 (15) (1999)
Stéphanie Héry, Daniel Genest, Jeremy C. Smith
Fluctuation and Correlation in Crystalline Lysozyme. J. Chem. Inf. Comput. Sci. 37 (6) (1997)
Jérôme Baudry, Serge Crouzy, Benoît Roux, Jeremy C. Smith
Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics. J. Chem. Inf. Comput. Sci. 37 (6) (1997)
Fred J. Taylor, Glenn S. Zelniker, Jeremy C. Smith, Jon Mellott
The Gauss machine-a DSP processor with a high RNS content. ICASSP (1991)