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2020 – today
- 2023
[j38]Yue Shen
, Jerry M. Parks, Jeremy C. Smith:
HLA-Clus: HLA class I clustering based on 3D structure. BMC Bioinform. 24(1): 189 (2023)- [j37]Rupesh Agarwal, Rajitha Rajeshwar T., Jeremy C. Smith:
Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J. Chem. Inf. Model. 63(23): 7444-7452 (2023) - 2022
- [j36]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): 3627-3637 (2022) - 2021
- [j35]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): 7-16 (2021) - [j34]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): 355-369 (2021) - 2020
- [j33]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): 147-155 (2020) - [j32]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): 528-537 (2020) - [j31]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:
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60(12): 5832-5852 (2020) - [c6]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: 43:1-43:10
2010 – 2019
- 2019
- [c5]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: 397-417 - [c4]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: 514-527 - 2015
- [j30]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: 33-43 (2015) - [j29]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): 721-726 (2015) - 2014
- [j28]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): 1268-1277 (2014) - 2013
- [j27]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): 845-854 (2013) - [j26]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): 2212-2221 (2013) - [j25]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): 3297-3307 (2013) - 2012
- [j24]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): 1491-1501 (2012) - [j23]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): 1207-1214 (2012) - [j22]Tomasz Berezniak, Andres Jäschke, Jeremy C. Smith, Petra Imhof:
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study. J. Comput. Chem. 33(19): 1603-1614 (2012) - 2011
- [j21]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): 1202-1209 (2011) - [j20]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): 545-567 (2011) - [j19]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) - [j18]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) - 2010
- [j17]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)
2000 – 2009
- 2009
- [j16]Kei Moritsugu, Jeremy C. Smith:
REACH: A program for coarse-grained biomolecular simulation. Comput. Phys. Commun. 180(7): 1188-1195 (2009) - [j15]Loukas Petridis, Jeremy C. Smith:
A molecular mechanics force field for lignin. J. Comput. Chem. 30(3): 457-467 (2009) - 2008
- [j14]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): 1429-1439 (2008) - 2006
- [j13]Frank Noé, Marcus Oswald, Gerhard Reinelt, Stefan Fischer, Jeremy C. Smith:
Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the AlphaL \leftrightharpoons Beta \leftrightharpoons AlphaR Transitions in Octaalanine. Multiscale Model. Simul. 5(2): 393-419 (2006) - [c3]Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith:
Clustering Analysis of Competitive Learning Network for Molecular Data. ISNN (1) 2006: 1244-1249 - [c2]Lin Wang, Minghu Jiang, Yinghua Lu, Frank Noé, Jeremy C. Smith:
Self-Organizing Map Clustering Analysis for Molecular Data. ISNN (1) 2006: 1250-1255 - 2005
- [j12]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): 34-42 (2005) - [j11]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): 1359-1371 (2005) - [j10]Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann:
A molecular mechanics force field for biologically important sterols. J. Comput. Chem. 26(13): 1383-1399 (2005) - [j9]Franci Merzel, Jeremy C. Smith:
High-Density Hydration Layer of Lysozymes: Molecular Dynamics Decomposition of Solution Scattering Data. J. Chem. Inf. Model. 45(6): 1593-1599 (2005) - [j8]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): 201-210 (2005) - 2003
- [j7]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): 187-196 (2003) - [j6]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): 632-639 (2003) - 2002
- [j5]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): 1143-1149 (2002) - 2001
- [j4]Jeremy C. Smith:
An anti-snapback circuit technique for inhibiting parasitic bipolar conduction during EOS/ESD events. Microelectron. Reliab. 41(3): 349-357 (2001)
1990 – 1999
- 1999
- [j3]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): 1644-1658 (1999) - 1997
- [j2]Stéphanie Héry, Daniel Genest, Jeremy C. Smith:
Fluctuation and Correlation in Crystalline Lysozyme. J. Chem. Inf. Comput. Sci. 37(6): 1011-1017 (1997) - [j1]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): 1018-1024 (1997) - 1991
- [c1]Fred J. Taylor, Glenn S. Zelniker, Jeremy C. Smith, Jon Mellott:
The Gauss machine-a DSP processor with a high RNS content. ICASSP 1991: 1081-1084
Coauthor Index
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