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)

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)

Classical force field parameters for the heme prosthetic group of cytochrome c. - Felix Autenrieth; Emad Tajkhorshid; Jérôme Baudry; Zaida Luthey-Schulten (J. Comput. Chem., 2004)

Determining anion-quadrupole interactions among protein, DNA, and ligand molecules. - Jason B. Harris; David D. Jenkins; Jonathan Reyles; Stephanie Rickett; Jordan M. Utley; Elizabeth E. Howell; Jérôme Baudry; Robert J. Hinde (BMC Bioinform., 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)

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

STAAR: Statistical analysis of aromatic rings. - David D. Jenkins; Jason B. Harris; Elizabeth E. Howell; Robert J. Hinde; Jérôme Baudry (J. Comput. Chem., 2013)

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein. - Davi R. Ortega; Guoya Mo; Kwangwoon Lee; Hongjun Zhou; Jérôme Baudry; Frederick W. Dahlquist; Igor B. Zhulin (PLoS Comput. Biol., 2013)

High-throughput virtual molecular docking with AutoDockCloud. - Sally R. Ellingson; Jérôme Baudry (Concurr. Comput. Pract. Exp., 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)

Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex. - Karan Kapoor; Nicole McGill; Cynthia B. Peterson; Harold V. Meyers; Michael N. Blackburn; Jérôme Baudry (J. Chem. Inf. Model., 2016)

Novel K-Means Clustering-based Undersampling and Feature Selection for Drug Discovery Applications. - Vishnu Sripriya Akondi; Vineetha Menon; Jérôme Baudry; Jana Whittle (BIBM, 2019)

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)

The Convergence of HPC, AI and Big Data in Rapid-Response to the COVID-19 Pandemic. - Sreenivas R. Sukumar 001; Jacob A. Balma; Christopher D. Rickett; Kristyn J. Maschhoff; Joseph Landman; Charles R. Yates; Amar G. Chittiboyina; Yuri K. Peterson; Aaron Vose; Kendall G. Byler; Jérôme Baudry; Ikhlas A. Khan (SMC, 2021)

Wavelet-based Spectral Analysis For Protein Conformation Selection and Prediction Using AI in Drug Discovery Applications. - Shivangi Gupta; Vineetha Menon; Jérôme Baudry (BIBM, 2022)