An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. - Rommie E. Amaro; Riccardo Baron; James Andrew McCammon (J. Comput. Aided Mol. Des., 2008)

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. - Jacob D. Durrant; Rommie E. Amaro; Lei Xie 006; Michael D. Urbaniak; Michael A. J. Ferguson; Antti Haapalainen; Zhijun Chen; Anne Marie Di Guilmi; Frank Wunder; Philip E. Bourne; James Andrew McCammon (PLoS Comput. Biol., 2010)

Modeling the pharmacodynamics of passive membrane permeability. - Robert V. Swift; Rommie E. Amaro (J. Comput. Aided Mol. Des., 2011)

Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants. - Özlem Demir; Roberta Baronio; Faezeh Salehi; Christopher D. Wassman; Linda Hall; G. Wesley Hatfield; Richard Chamberlin; Peter Kaiser; Richard H. Lathrop; Rommie E. Amaro (PLoS Comput. Biol., 2011)

Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2. - Özlem Demir; Rommie E. Amaro (J. Chem. Inf. Model., 2012)

Multistructural hot spot characterization with FTProd. - Lane Votapka; Rommie E. Amaro (Bioinform., 2013)

Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding. - Jiho Park; Luke Czapla; Rommie E. Amaro (J. Chem. Inf. Model., 2013)

Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations. - Pek U. Ieong; Jesper Sørensen; Prasantha L. Vemu; Celia W. Wong; Özlem Demir; Nadya P. Williams; Jianwu Wang 001; Daniel Crawl; Robert V. Swift; Robert D. Malmstrom; Ilkay Altintas; Rommie E. Amaro (ICCS, 2014)

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. - Jacob D. Durrant; Rommie E. Amaro (BMC Bioinform., 2014)

LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. - Jacob D. Durrant; Rommie E. Amaro (PLoS Comput. Biol., 2014)

Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. - Jacob D. Durrant; Kathryn E. Carlson; Teresa A. Martin; Tavina L. Offutt; Christopher G. Mayne; John A. Katzenellenbogen; Rommie E. Amaro (J. Chem. Inf. Model., 2015)

A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. - Nur Kusaira Khairul Ikram; Jacob D. Durrant; Muchtaridi Muchtaridi; Ayunni Salihah Zalaludin; Neny Purwitasari; Nornisah Mohamed; Aisyah Saad Abdul Rahim; Chan Kit Lam; Yahaya M. Normi; Noorsaadah Abdul Rahman; Rommie E. Amaro; Habibah A. Wahab (J. Chem. Inf. Model., 2015)

Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. - Lane W. Votapka; Rommie E. Amaro (PLoS Comput. Biol., 2015)

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. - Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A. Stuckey; You-Na Kang; Jim Delproposto; Ginger Kubish; James B. Dunbar Jr.; Heather A. Carlson; Stephen K. Burley; W. Patrick Walters; et al. (J. Comput. Aided Mol. Des., 2016)

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. - Christopher T. Lee; Jeffrey Comer; Conner Herndon; Nelson Leung 003; Anna Pavlova; Robert V. Swift; Chris Tung; Christopher N. Rowley; Rommie E. Amaro; Christophe Chipot; Yi Wang; James C. Gumbart (J. Chem. Inf. Model., 2016)

Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. - Tavina L. Offutt; Robert V. Swift; Rommie E. Amaro (J. Chem. Inf. Model., 2016)

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. - Robert V. Swift; Siti Azma Jusoh; Tavina L. Offutt; Eric S. Li; Rommie E. Amaro (J. Chem. Inf. Model., 2016)

Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research. - Shweta Purawat; Charles Cowart; Rommie E. Amaro; Ilkay Altintas (J. Comput. Sci., 2017)

Exascale Computing: A New Dawn for Computational Biology. - Christopher T. Lee; Rommie E. Amaro (Comput. Sci. Eng., 2018)

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Zied Gaieb; Shuai Liu; Symon Gathiaka; Michael Chiu; Huanwang Yang; Chenghua Shao; Victoria A. Feher; W. Patrick Walters; Bernd Kuhn; Markus G. Rudolph; Stephen K. Burley; Michael K. Gilson; et al. (J. Comput. Aided Mol. Des., 2018)

Women in Computational Chemistry. - Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia (J. Chem. Inf. Model., 2018)

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. - Zied Gaieb; Conor D. Parks; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Millard H. Lambert; Neysa Nevins; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; Stephen K. Burley; et al. (J. Comput. Aided Mol. Des., 2019)

Frontiers in CryoEM Modeling. - Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E. Amaro (J. Chem. Inf. Model., 2019)

Determinants of Oligonucleotide Selectivity of APOBEC3B. - Jeffrey R. Wagner; Özlem Demir; Michael A. Carpenter; Hideki Aihara; Daniel A. Harki; Reuben S. Harris; Rommie E. Amaro (J. Chem. Inf. Model., 2019)

A Celebration of Women in Computational Chemistry. - Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia (J. Chem. Inf. Model., 2019)

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. - Pei-Chi Yang; Shweta Purawat; Pek U. Ieong; Mao-Tsuen Jeng; Kevin R. DeMarco; Igor Vorobyov; Andrew D. McCulloch; Ilkay Altintas; Rommie E. Amaro; Colleen E. Clancy (PLoS Comput. Biol., 2019)

The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. - Christopher T. Lee; John B. Moody; Rommie E. Amaro; James Andrew McCammon; Michael J. Holst (ACM Trans. Math. Softw., 2019)

Biomolecular Simulations in the Time of COVID-19, and After. - Rommie E. Amaro; Adrian J. Mulholland (Comput. Sci. Eng., 2020)

Drug Design Data Resource, Grand Challenge 4, second of two issues. - Michael K. Gilson; Rommie E. Amaro (J. Comput. Aided Mol. Des., 2020)

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Conor D. Parks; Zied Gaieb; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Johanna M. Jansen; Georgia B. McGaughey; Richard A. Lewis; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; et al. (J. Comput. Aided Mol. Des., 2020)

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. - Surl-Hee Ahn; Benjamin R. Jagger; Rommie E. Amaro (J. Chem. Inf. Model., 2020)

A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. - Rommie E. Amaro; Adrian J. Mulholland (J. Chem. Inf. Model., 2020)

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. - Angelica Mazzolari; Ariane Nunes-Alves; Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2020)

Editorial: Method and Data Sharing and Reproducibility of Scientific Results. - Kenneth M. Merz Jr.; Rommie E. Amaro; Zoe Cournia; Matthias Rarey; Thereza A. Soares; Alexander Tropsha; Habibah A. Wahab; Renxiao Wang (J. Chem. Inf. Model., 2020)

COVID19 - Computational Chemists Meet the Moment. - Adrian J. Mulholland; Rommie E. Amaro (J. Chem. Inf. Model., 2020)

Faces of Contemporary CryoEM Information and Modeling. - Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E. Amaro (J. Chem. Inf. Model., 2020)

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. - Christopher T. Lee; Justin G. Laughlin; Nils Angliviel de La Beaumelle; Rommie E. Amaro; James Andrew McCammon; Ravi Ramamoorthi; Michael J. Holst; Padmini Rangamani (PLoS Comput. Biol., 2020)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

Advancing Women in Chemistry. - Zoe Cournia; Thereza A. Soares; Habibah A. Wahab; Rommie E. Amaro (J. Chem. Inf. Model., 2021)

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. - Terra Sztain; Rommie E. Amaro; James Andrew McCammon (J. Chem. Inf. Model., 2021)

Benchmarking ensemble docking methods in D3R Grand Challenge 4. - Jessie Low Gan; Dhruv Kumar 006; Cynthia Chen; Bryn C. Taylor; Benjamin R. Jagger; Rommie E. Amaro; Christopher T. Lee (J. Comput. Aided Mol. Des., 2022)

Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. - Zoe Cournia; Thereza A. Soares; Habibah A. Wahab; Rommie E. Amaro (J. Chem. Inf. Model., 2022)

SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. - Lane W. Votapka; Andrew M. Stokely; Anupam Anand Ojha; Rommie E. Amaro (J. Chem. Inf. Model., 2022)

Voyager - An Innovative Computational Resource for Artificial Intelligence & Machine Learning Applications in Science and Engineering. - Rommie E. Amaro; Jiunn-Yeu Chen; Javier M. Duarte; Thomas E. Hutton; Christopher Irving; Martin C. Kandes; Amit Majumdar 001; Dmitry Y. Mishin; Mai H. Nguyen; Paul Rodríguez; Fernando Silva; Robert S. Sinkovits; et al. (PEARC, 2023)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. - Anupam Anand Ojha; Ambuj Srivastava; Lane W. Votapka; Rommie E. Amaro (J. Chem. Inf. Model., 2023)

Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. - Thereza A. Soares; Zoe Cournia; Kevin J. Naidoo; Rommie E. Amaro; Habibah A. Wahab; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins. - Fiona L. Kearns; Mia A. Rosenfeld; Rommie E. Amaro (J. Chem. Inf. Model., 2024)

Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. - Jie Li 072; Oufan Zhang; Kunyang Sun; Yingze Wang; Xingyi Guan; Dorian Bagni; Mojtaba Haghighatlari; Fiona L. Kearns; Conor D. Parks; Rommie E. Amaro; Teresa Head-Gordon (J. Chem. Inf. Model., 2024)

NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. - Andrew M. Stokely; Lane W. Votapka; Marcus T. Hock; Abigail E. Teitgen; James Andrew McCammon; Andrew D. McCulloch; Rommie E. Amaro (J. Chem. Inf. Model., 2024)

Regulatory Interactions between APOBEC3B N- and C-Terminal Domains. - Mac Kevin E. Braza; Özlem Demir; Surl-Hee Ahn; Clare Morris; Carla Calvó-Tusell; Kelly L. McGuire; Bárbara de la Peña Avalos; Michael A. Carpenter; Yanjun Chen; Lorenzo Casalino; Hideki Aihara; Mark A. Herzik; et al. (J. Chem. Inf. Model., 2025)