Jeremy C. Smith

According to our database, Jeremy C. Smith authored at least 44 papers between 1991 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking.

Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith

J. Chem. Inf. Model., December, 2023

HLA-Clus: HLA class I clustering based on 3D structure.

Yue Shen, Jerry M. Parks, Jeremy C. Smith

BMC Bioinform., December, 2023

2022

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

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

Supercomputing Pipelines Search for Therapeutics Against COVID-19.

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

Comput. Sci. Eng., 2021

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, 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

J. Chem. Inf. Model., 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

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

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, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

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

Proceedings of the High Performance Computing, 2019

Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions.

John R. Ossyra, Ada Sedova, Matthew B. Baker, Jeremy C. Smith

Proceedings of the High Performance Computing, 2019

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

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

2014

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

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

VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers.

Sally R. Ellingson, Jeremy C. Smith, Jérôme Baudry

J. Comput. Chem., 2013

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

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

Stereoselection in the diels-alderase ribozyme: A molecular dynamics study.

Tomasz Berezniak, Andres Jäschke, Jeremy C. Smith, Petra Imhof

J. Comput. Chem., 2012

Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers.

Benjamin Lindner, Jeremy C. Smith

Comput. Phys. Commun., 2012

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

Role of Histone Tails in Structural Stability of the Nucleosome.

Mithun Biswas, Karine Voltz, Jeremy C. Smith, Jörg Langowski

PLoS Comput. Biol., 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

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

2010

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

2009

A molecular mechanics force field for lignin.

Loukas Petridis, Jeremy C. Smith

J. Comput. Chem., 2009

REACH: A program for coarse-grained biomolecular simulation.

Kei Moritsugu, Jeremy C. Smith

Comput. Phys. Commun., 2009

2008

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

2006

Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the <i>Alpha_L</i> \leftrightharpoons <i>Beta</i> \leftrightharpoons <i>Alpha_R</i> Transitions in Octaalanine.

Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith

Multiscale Model. Simul., 2006

Self-Organizing Map Clustering Analysis for Molecular Data.

Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith

Proceedings of the Advances in Neural Networks - ISNN 2006, Third International Symposium on Neural Networks, Chengdu, China, May 28, 2006

Clustering Analysis of Competitive Learning Network for Molecular Data.

Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith

Proceedings of the Advances in Neural Networks - ISNN 2006, Third International Symposium on Neural Networks, Chengdu, China, May 28, 2006

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

High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data.

Franci Merzel, Jeremy C. Smith

J. Chem. Inf. Model., 2005

Nonuniform charge scaling (NUCS): A practical approximation of solvent electrostatic screening in proteins.

Sonja M. Schwarzl, Danzhi Huang, Jeremy C. Smith, Stefan Fischer

J. Comput. Chem., 2005

A molecular mechanics force field for biologically important sterols.

Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann

J. Comput. Chem., 2005

AFMM: A molecular mechanics force field vibrational parametrization program.

Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith

Comput. Phys. Commun., 2005

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

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

Silico Biol., 2003

2002

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

J. Comput. Chem., 2002

2001

An anti-snapback circuit technique for inhibiting parasitic bipolar conduction during EOS/ESD events.

Jeremy C. Smith

Microelectron. Reliab., 2001

1999

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

1997

Fluctuation and Correlation in Crystalline Lysozyme.

Stéphanie Héry, Daniel Genest, Jeremy C. Smith

J. Chem. Inf. Comput. Sci., 1997

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

1991

The Gauss machine-a DSP processor with a high RNS content.

Fred J. Taylor, Glenn S. Zelniker, Jeremy C. Smith, Jon Mellott

Proceedings of the 1991 International Conference on Acoustics, 1991