Rommie Elizabeth Amaro (Rommie Amaro, Rommie E Amaro)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 91

Top Topics

Respiratory Syndrome Coronavirus

Top Venues

Journal of chemical information and modeling

bioRxiv : the preprint server for biology

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L Tse, Anupam A Ojha, Fiona L Kearns, Mia A Rosenfeld, Emily Happy Miller, Cory M Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S Mclellan, Rommie Elizabeth Amaro
Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nature communications 15 (1) (2024)
Jie Li, Oufan Zhang, Kunyang Sun, Yingze Wang, Xingyi Guan, Dorian Bagni, Mojtaba Haghighatlari, Fiona L Kearns, Doraiswami Ramkrishna, Rommie Elizabeth Amaro, Teresa Head-Gordon
Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. Journal of chemical information and modeling (2024)
Abigail C Dommer, Mickey M Rogers, Kimberly A Carter-Fenk, Nicholas A Wauer, Patiemma Rubio, Aakash Davasam, Heather C Allen, Rommie Elizabeth Amaro
Interfacial Enrichment of Lauric Acid Assisted by Long-Chain Fatty Acids, Acidity and Salinity at Sea Spray Aerosol Surfaces. The journal of physical chemistry. A 128 (34) (2024)
Katherine F M Jones, Özlem Demir, Mackenzie K Wyllie, Michael J Grillo, Clare Morris, Sophia P Hirakis, Rahul Dadabhau Kardile, Michael A Walters, Reuben S Harris, Rommie Elizabeth Amaro, Daniel A Harki
Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening. bioRxiv : the preprint server for biology (2024)
John H Kim, Aashish Shivkumar, Masaki Norimoto, Sascha Castro Lingl, Christian G Seitz, Rommie Elizabeth Amaro, Steve L Gonias, Jerry Yang, Wendy M Campana
Binding and Activation of LRP1-Dependent Cell Signaling in Schwann Cells Using a Peptide Derived from the Hemopexin Domain of MMP-9. Biochemistry (2024)
Alexandra L Tse, Cory M Acreman, Inna Ricardo-Lax, Jacob Berrigan, Gorka Lasso, Toheeb Balogun, Fiona L Kearns, Lorenzo Casalino, Georgia L McClain, Amartya Mudry Chandran, Charlotte Lemeunier, Rommie Elizabeth Amaro, Charles M Rice, Rohit K Jangra, Jason S McLellan, Kartik Chandran, Emily Happy Miller
Epistasis between N-terminal and receptor-binding domains drives cell entry in a bat coronavirus spike. bioRxiv : the preprint server for biology (2024)
Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L Tse, Anupam A Ojha, Fiona L Kearns, Mia A Rosenfeld, Emily Happy Miller, Cory M Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S Mclellan, Rommie Elizabeth Amaro
Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nature communications 15 (1) (2024)
Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L Tse, Anupam A Ojha, Fiona L Kearns, Mia A Rosenfeld, Emily Happy Miller, Cory M Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S Mclellan, Rommie Elizabeth Amaro
Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nature communications 15 (1) (2024)
Abigail C Dommer, Mickey M Rogers, Kimberly A Carter-Fenk, Nicholas A Wauer, Patiemma Rubio, Aakash Davasam, Heather C Allen, Rommie Elizabeth Amaro
Interfacial Enrichment of Lauric Acid Assisted by Long-Chain Fatty Acids, Acidity and Salinity at Sea Spray Aerosol Surfaces. The journal of physical chemistry. A 128 (34) (2024)
John H Kim, Aashish Shivkumar, Masaki Norimoto, Sascha Castro Lingl, Christian G Seitz, Rommie Elizabeth Amaro, Steve L Gonias, Jerry Yang, Wendy M Campana
Binding and Activation of LRP1-Dependent Cell Signaling in Schwann Cells Using a Peptide Derived from the Hemopexin Domain of MMP-9. Biochemistry 63 (6) (2024)
Katherine F M Jones, Özlem Demir, Mackenzie K Wyllie, Michael J Grillo, Clare Morris, Sophia P Hirakis, Rahul Dadabhau Kardile, Michael A Walters, Reuben S Harris, Rommie Elizabeth Amaro, Daniel A Harki
Development of Allosteric Small Molecule APOBEC3B Inhibitors from In Silico Screening. bioRxiv : the preprint server for biology (2024)
John H Kim, Aashish Shivkumar, Masaki Norimoto, Sascha Castro Lingl, Christian G Seitz, Rommie Elizabeth Amaro, Steve L Gonias, Jerry Yang, Wendy M Campana
Binding and Activation of LRP1-Dependent Cell Signaling in Schwann Cells Using a Peptide Derived from the Hemopexin Domain of MMP-9. Biochemistry 63 (6) (2024)
Abigail C Dommer, Mickey M Rogers, Kimberly A Carter-Fenk, Nicholas A Wauer, Patiemma Rubio, Aakash Davasam, Heather C Allen, Rommie Elizabeth Amaro
Interfacial Enrichment of Lauric Acid Assisted by Long-Chain Fatty Acids, Acidity and Salinity at Sea Spray Aerosol Surfaces. The journal of physical chemistry. A (2024)
Xandra Nuqui, Lorenzo Casalino, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L Tse, Anupam A Ojha, Fiona L Kearns, Mia A Rosenfeld, Emily Happy Miller, Cory M Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S Mclellan, Rommie Elizabeth Amaro
Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens. Nature communications 15 (1) (2024)
Alexandra L Tse, Cory M Acreman, Inna Ricardo-Lax, Jacob Berrigan, Gorka Lasso, Toheeb Balogun, Fiona L Kearns, Lorenzo Casalino, Georgia L McClain, Amartya Mudry Chandran, Charlotte Lemeunier, Rommie Elizabeth Amaro, Charles M Rice, Rohit K Jangra, Jason S McLellan, Kartik Chandran, Emily Happy Miller
Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses. bioRxiv : the preprint server for biology (2024)
Anupam Anand Ojha, Ambuj Srivastava, Lane William Votapka, Rommie Elizabeth Amaro
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. Journal of chemical information and modeling (2023)
Anupam Anand Ojha, Lane William Votapka, Rommie Elizabeth Amaro
QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chemical science 14 (45) (2023)
Joann Chongsaritsinsuk, Alexandra D Steigmeyer, Keira E Mahoney, Mia A Rosenfeld, Taryn M Lucas, Deniz Ince, Fiona L Kearns, Alexandria S Battison, Marie A Hollenhorst, D Judy Shon, Katherine H Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R Bertozzi, Michael J Ferracane, Rommie Elizabeth Amaro, Stacy A Malaker
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. bioRxiv : the preprint server for biology (2023)
Katherine F M Jones, Mohamed Shehata, Michael A Carpenter, Rommie Elizabeth Amaro, Daniel A Harki
APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization. ACS medicinal chemistry letters 14 (3) (2023)
Seyed Arad Moghadasi, Emmanuel Heilmann, Ahmed Magdy Khalil, Christina Nnabuife, Fiona L Kearns, Chengjin Ye, Sofia N Moraes, Francesco Costacurta, Morgan A Esler, Hideki Aihara, Dorothee von Laer, Luis Martinez-Sobrido, Timothy G Palzkill, Rommie Elizabeth Amaro, Reuben Stewart Harris
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Science advances 9 (13) (2023)
Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Elizabeth Amaro
DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling. Journal of chemical theory and computation 19 (4) (2023)
Seyed Arad Moghadasi, Emmanuel Heilmann, Ahmed Magdy Khalil, Christina Nnabuife, Fiona L Kearns, Chengjin Ye, Sofia N Moraes, Francesco Costacurta, Morgan A Esler, Hideki Aihara, Dorothee von Laer, Luis Martinez-Sobrido, Timothy G Palzkill, Rommie Elizabeth Amaro, Reuben Stewart Harris
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Science advances 9 (13) (2023)
Abigail C Dommer, Nicholas A Wauer, Kyle J Angle, Aakash Davasam, Patiemma Rubio, Man Luo, Clare K Morris, Kimberly A Prather, Vicki H Grassian, Rommie Elizabeth Amaro
Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology. ACS central science 9 (6) (2023)
Joann Chongsaritsinsuk, Alexandra D Steigmeyer, Keira E Mahoney, Mia A Rosenfeld, Taryn M Lucas, Deniz Ince, Fiona L Kearns, Alexandria S Battison, Marie A Hollenhorst, D Judy Shon, Katherine H Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R Bertozzi, Michael J Ferracane, Rommie Elizabeth Amaro, Stacy A Malaker
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. bioRxiv : the preprint server for biology (2023)
Joann Chongsaritsinsuk, Alexandra D Steigmeyer, Keira E Mahoney, Mia A Rosenfeld, Taryn M Lucas, Deniz Ince, Fiona L Kearns, Alexandria S Battison, Marie A Hollenhorst, D Judy Shon, Katherine H Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R Bertozzi, Michael J Ferracane, Rommie Elizabeth Amaro, Stacy A Malaker
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. bioRxiv : the preprint server for biology (2023)
Thereza A Soares, Zoe Cournia, Kevin J Naidoo, Rommie Elizabeth Amaro, Habibah Abdul Wahab, Kenneth M Merz
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. Journal of chemical information and modeling (2023)
Marcus T Hock, Abigail E Teitgen, Kimberly J McCabe, Sophia P Hirakis, Gary A Huber, Michael Regnier, Rommie Elizabeth Amaro, James Andrew McCammon, Andrew D McCulloch
Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling. Journal of applied physics 134 (7) (2023)
Joann Chongsaritsinsuk, Alexandra D Steigmeyer, Keira E Mahoney, Mia A Rosenfeld, Taryn M Lucas, Courtney M Smith, Alice Li, Deniz Ince, Fiona L Kearns, Alexandria S Battison, Marie A Hollenhorst, D Judy Shon, Katherine H Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R Bertozzi, Michael J Ferracane, Mark A Lemmon, Rommie Elizabeth Amaro, Stacy A Malaker
Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nature communications 14 (1) (2023)
Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Elizabeth Amaro
DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling. Journal of chemical theory and computation (2023)
Seyed Arad Moghadasi, Emmanuel Heilmann, Ahmed Magdy Khalil, Christina Nnabuife, Fiona L Kearns, Chengjin Ye, Sofia N Moraes, Francesco Costacurta, Morgan A Esler, Hideki Aihara, Dorothee von Laer, Luis Martinez-Sobrido, Timothy G Palzkill, Rommie Elizabeth Amaro, Reuben Stewart Harris
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. Science advances 9 (13) (2023)
Anupam Anand Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Elizabeth Amaro
DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling. Journal of chemical theory and computation (2023)
Chang-Ki Oh, Tomohiro Nakamura, Nathan Beutler, Xu Zhang, Juan Piña-Crespo, Maria Talantova, Swagata Ghatak, Dorit Trudler, Lauren N Carnevale, Scott R McKercher, Malina A Bakowski, Jolene K Diedrich, Amanda J Roberts, Ashley K Woods, Victor Chi, Anil K Gupta, Mia A Rosenfeld, Fiona L Kearns, Lorenzo Casalino, Namir Shaabani, Hejun Liu, Ian A Wilson, Rommie Elizabeth Amaro, Dennis R Burton, John Yates Iii, Cyrus Becker, Thomas F Rogers, Arnab K Chatterjee, Stuart A Lipton
Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nature chemical biology (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Seyed Arad Moghadasi, Emmanuel Heilmann, Sofia N Moraes, Fiona L Kearns, Dorothee von Laer, Rommie Elizabeth Amaro, Reuben Stewart Harris
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors. bioRxiv : the preprint server for biology (2022)
Lorenzo Casalino, Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A Wilson, Masaru Kanekiyo, Rommie Elizabeth Amaro
Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS central science 8 (12) (2022)
Kyle J Angle, Christopher M Nowak, Aakash Davasam, Abigail C Dommer, Nicholas A Wauer, Rommie Elizabeth Amaro, Vicki H Grassian
Amino Acids Are Driven to the Interface by Salts and Acidic Environments. The journal of physical chemistry letters 13 (12) (2022)
Lorenzo Casalino, Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A Wilson, Masaru Kanekiyo, Rommie Elizabeth Amaro
Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS central science 8 (12) (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Nicholas H Moeller, Ke Shi, Özlem Demir, Christopher Belica, Surajit Banerjee, Lulu Yin, Cameron Durfee, Rommie Elizabeth Amaro, Hideki Aihara
Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proceedings of the National Academy of Sciences of the United States of America 119 (9) (2022)
Thomas G Laughlin, Amar Deep, Amy M Prichard, Christian G Seitz, Yajie Gu, Eray Enustun, Sergey Suslov, Kanika Khanna, Erica A Birkholz, Emily Armbruster, James Andrew McCammon, Rommie Elizabeth Amaro, Joe Pogliano, Kevin D Corbett, Elizabeth Villa
Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 608 (7922) (2022)
Zoe Cournia, Thereza A Soares, Habibah Abdul Wahab, Rommie Elizabeth Amaro
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. Journal of chemical information and modeling 62 (24) (2022)
Chang-Ki Oh, Tomohiro Nakamura, Nathan Beutler, Xu Zhang, Juan Piña-Crespo, Maria Talantova, Swagata Ghatak, Dorit Trudler, Lauren N Carnevale, Scott R McKercher, Malina A Bakowski, Jolene K Diedrich, Amanda J Roberts, Ashley K Woods, Victor Chi, Anil K Gupta, Mia A Rosenfeld, Fiona L Kearns, Lorenzo Casalino, Namir Shaabani, Hejun Liu, Ian A Wilson, Rommie Elizabeth Amaro, Dennis R Burton, John R Yates, Cyrus Becker, Thomas F Rogers, Arnab K Chatterjee, Stuart A Lipton
Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection. bioRxiv : the preprint server for biology (2022)
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia A Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John D Russo, Ana Sofia F Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel Ga Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'Connor, Frederick Manby, Anima Anandkumar, David Hardy, James C Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel M Zuckerman, Adrian J Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. The international journal of high performance computing applications 37 (1) (2022)
Lorenzo Casalino, Christian Seitz, Julia Lederhofer, Yaroslav Tsybovsky, Ian A Wilson, Masaru Kanekiyo, Rommie Elizabeth Amaro
Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities. ACS central science 8 (12) (2022)
Matthew M Copeland, Hung N Do, Lane William Votapka, Keya Joshi, Jinan Wang, Rommie Elizabeth Amaro, Yinglong Miao
Gaussian Accelerated Molecular Dynamics in OpenMM. The journal of physical chemistry. B 126 (31) (2022)
John M Herbert, Martin Head-Gordon, Hrant P Hratchian, Teresa Head-Gordon, Rommie Elizabeth Amaro, Alán Aspuru-Guzik, Roald Hoffmann, Carol A Parish, Christina M Payne, Troy Van Voorhis
Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence. The journal of physical chemistry letters 13 (30) (2022)
Lane W Votapka, Andrew M Stokely, Anupam Anand Ojha, Rommie Elizabeth Amaro
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. Journal of chemical information and modeling 62 (13) (2022)
Zoe Cournia, Thereza A Soares, Habibah Abdul Wahab, Rommie Elizabeth Amaro
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. Journal of chemical information and modeling 62 (24) (2022)
Emanuele Andreano, Giulia Piccini, Danilo Licastro, Lorenzo Casalino, Nicole V Johnson, Ida Paciello, Simeone Dal Monego, Elisa Pantano, Noemi Manganaro, Alessandro Manenti, Rachele Manna, Elisa Casa, Inesa Hyseni, Linda Benincasa, Emanuele Montomoli, Rommie Elizabeth Amaro, Jason S McLellan, Rino Rappuoli
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma. Proceedings of the National Academy of Sciences of the United States of America 118 (36) (2021)
Surl-Hee Ahn, Anupam Anand Ojha, Rommie Elizabeth Amaro, James Andrew McCammon
Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling. Journal of chemical theory and computation (2021)
Terra Sztain, Rommie Elizabeth Amaro, James Andrew McCammon
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. Journal of chemical information and modeling 61 (7) (2021)
Adrian J Mulholland, Rommie Elizabeth Amaro
COVID19 - Computational Chemists Meet the Moment. Journal of chemical information and modeling 60 (12) (2021)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie Elizabeth Amaro
Faces of Contemporary CryoEM Information and Modeling. Journal of chemical information and modeling 60 (5) (2021)
Kenneth M Merz, Rommie Elizabeth Amaro, Zoe Cournia, Matthias Rarey, Thereza A Soares, Alexander Trospsha, Habibah Abdul Wahab, Ren-Xiao Wang
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. Journal of chemical information and modeling 60 (12) (2021)
Jason C Klima, Lindsey A Doyle, Justin Daho Lee, Michael Rappleye, Lauren A Gagnon, Min Yen Lee, Emilia P Barros, Anastassia Andreevna Vorobieva, Jiayi Dou, Samantha B Bremner, Jacob S Quon, Cameron M Chow, Lauren Carter, David L Mack, Rommie Elizabeth Amaro, Joshua C Vaughan, Andre Berndt, Barry L Stoddard, Julien S Baker
Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nature communications 12 (1) (2021)
Christopher Lee, Abigail C Dommer, Jamie M Schiffer, Rommie Elizabeth Amaro, Vicki H Grassian, Kimberly A Prather
Cation-Driven Lipopolysaccharide Morphological Changes Impact Heterogeneous Reactions of Nitric Acid with Sea Spray Aerosol Particles. The journal of physical chemistry letters 12 (20) (2021)
Terra Sztain, Surl-Hee Ahn, Anthony T Bogetti, Lorenzo Casalino, Jory A Goldsmith, Evan Seitz, Ryan S McCool, Fiona L Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, James Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason S McLellan, Lillian T Chong, Rommie Elizabeth Amaro
A glycan gate controls opening of the SARS-CoV-2 spike protein. Nature chemistry 13 (10) (2021)
Alex Muthengi, Virangika K Wimalasena, Hailemichael O Yosief, Melissa J Bikowitz, Logan H Sigua, Tingjian Wang, Deyao Li, Zied Gaieb, Gagan Dhawan, Shuai Liu, Jon Erickson, Rommie Elizabeth Amaro, Ernst K Schonbrunn, Jun Qi, Wei Zhang
Development of Dimethylisoxazole-Attached Imidazo[1,2-a]pyridines as Potent and Selective CBP/P300 Inhibitors. Journal of medicinal chemistry 64 (9) (2021)
Sang Hoon Kim, Fiona L Kearns, Mia A Rosenfeld, Lorenzo Casalino, Micah J Papanikolas, Carlos L Simmerling, Rommie Elizabeth Amaro, Ronit Freeman
GlycoGrip : Cell Surface-Inspired Universal Sensor for Betacoronaviruses. ACS central science 8 (1) (2021)
Abigail C Dommer, Lorenzo Casalino, Fiona L Kearns, Mia A Rosenfeld, Nicholas A Wauer, Surl-Hee Ahn, John D Russo, Sofia Oliveira, Clare Morris, Anthony T Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G A Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick R Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E Stone, Daniel M Zuckerman, Adrian Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. bioRxiv : the preprint server for biology (2021)
Zoe Cournia, Thereza A Soares, Habibah Abdul Wahab, Rommie Elizabeth Amaro
Advancing Women in Chemistry. Journal of chemical information and modeling 61 (11) (2021)
Tim Hempel, Mauricio J Del Razo, Christopher T Lee, Bryn C Taylor, Rommie Elizabeth Amaro, Frank Noé
Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes. Proceedings of the National Academy of Sciences of the United States of America 118 (31) (2021)
Man Luo, Nicholas A Wauer, Kyle J Angle, Abigail C Dommer, Meishi Song, Christopher M Nowak, Rommie Elizabeth Amaro, Vicki H Grassian
Insights into the behavior of nonanoic acid and its conjugate base at the air/water interface through a combined experimental and theoretical approach. Chemical science 11 (39) (2020)
Angelica Mazzolari, Ariane Nunes Alves, Habibah Abdul Wahab, Rommie Elizabeth Amaro, Zoe Cournia, Kenneth M Merz
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. Journal of chemical information and modeling 60 (7) (2020)
Rommie Elizabeth Amaro, Adrian J Mulholland
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. Journal of chemical information and modeling 60 (6) (2020)
Alvin Yu, Alexander J Pak, Peng He, Viviana Monje-Galvan, Lorenzo Casalino, Zied Gaieb, Abigail C Dommer, Rommie Elizabeth Amaro, Gregory A Voth
A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. bioRxiv : the preprint server for biology (2020)
Christopher T Lee, Justin G Laughlin, Nils Angliviel de La Beaumelle, Rommie Elizabeth Amaro, J Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS computational biology 16 (4) (2020)
Habibah Abdul Wahab, Rommie Elizabeth Amaro, Zoe Cournia
A Celebration of Women in Computational Chemistry. Journal of chemical information and modeling 59 (5) (2020)
Benjamin R Jagger, Anupam Anand Ojha, Rommie Elizabeth Amaro
Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach. Journal of chemical theory and computation 16 (8) (2020)
Conor D Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W Patrick Walters, Johanna M Jansen, Georgia McGaughey, Richard A Lewis, Scott D Bembenek, Michael K Ameriks, Tara Mirzadegan, Stephen K Burley, Rommie Elizabeth Amaro, Michael K Gilson
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. Journal of computer-aided molecular design 34 (2) (2020)
Surl-Hee Ahn, Benjamin R Jagger, Rommie Elizabeth Amaro
Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. Journal of chemical information and modeling 60 (11) (2020)
Emilia P Barros, Özlem Demir, Jenaro Soto, Melanie J Cocco, Rommie Elizabeth Amaro
Markov state models and NMR uncover an overlooked allosteric loop in p53. Chemical science 12 (5) (2020)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie Elizabeth Amaro
Frontiers in CryoEM Modeling. Journal of chemical information and modeling 59 (7) (2019)
Mattia Bernetti, Matteo Masetti, Maurizio Recanatini, Rommie Elizabeth Amaro, Andrea Cavalli
An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes. Journal of chemical theory and computation 15 (10) (2019)
Man Luo, Abigail C Dommer, Jamie M Schiffer, Donald J Rez, Andrew R Mitchell, Rommie Elizabeth Amaro, Vicki H Grassian
Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at Marine-Relevant Aerosol Surfaces. Langmuir : the ACS journal of surfaces and colloids 35 (27) (2019)
Emilia P Barros, Jamie M Schiffer, Anastassia Vorobieva, Jiayi Dou, David Baker, Rommie Elizabeth Amaro
Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations. Journal of chemical theory and computation 15 (10) (2019)
Bryn C Taylor, Christopher T Lee, Rommie Elizabeth Amaro
Structural basis for ligand modulation of the CCR2 conformational landscape. Proceedings of the National Academy of Sciences of the United States of America 116 (17) (2019)
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, Rommie Elizabeth Amaro, Michael K Gilson
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. Journal of computer-aided molecular design 33 (1) (2019)
Benjamin R Jagger, Christopher T Lee, Rommie Elizabeth Amaro
Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. The journal of physical chemistry letters 9 (17) (2018)
Jeffrey R Wagner, Özlem Demir, Michael A Carpenter, Hideki Aihara, Daniel A Harki, Reuben S Harris, Rommie Elizabeth Amaro
Determinants of Oligonucleotide Selectivity of APOBEC3B. Journal of chemical information and modeling 59 (5) (2018)
Rommie Elizabeth Amaro, Elizabeth Villa, Zan Luthey-Schulten
Biography of Klaus Schulten. The journal of physical chemistry. B 121 (15) (2018)
Habibah Abdul Wahab, Rommie Elizabeth Amaro, Zoe Cournia
Women in Computational Chemistry. Journal of chemical information and modeling 58 (11) (2018)
Maria Carmen Mulero, Shandy Shahabi, Myung Soo Ko, Jamie M Schiffer, De-Bin Huang, Vivien Ya-Fan Wang, Rommie Elizabeth Amaro, Tom Huxford, Gourisankar Ghosh
Protein Cofactors Are Essential for High-Affinity DNA Binding by the Nuclear Factor κB RelA Subunit. Biochemistry 57 (20) (2018)
Tavina L Offutt, Pek U Ieong, Özlem Demir, Rommie Elizabeth Amaro
Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. Biochemistry 57 (46) (2018)
Gabriel Castro-Falcón, Grant S Seiler, Özlem Demir, Manoj K Rathinaswamy, David Hamelin, Reece M Hoffmann, Stefanie L Makowski, Anne-Catrin Letzel, Seth J Field, John E Burke, Rommie Elizabeth Amaro, Chambers C Hughes
Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. Journal of medicinal chemistry 61 (23) (2018)
Sophia P Hirakis, Robert D Malmstrom, Rommie Elizabeth Amaro
Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry 56 (30) (2017)
Emília P Barros, Robert D Malmstrom, Kimya Nourbakhsh, Jason C Del Rio, Alexandr P Kornev, Susan S Taylor, Rommie Elizabeth Amaro
Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα. Biochemistry 56 (10) (2017)
Ke Shi, Özlem Demir, Michael A Carpenter, Jeff Wagner, Kayo Kurahashi, Reuben S Harris, Rommie Elizabeth Amaro, Hideki Aihara
Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. Scientific reports 7 (1) (2017)
Jeffrey R Wagner, Jesper Sørensen, Nathan Hensley, Celia Wong, Clare Zhu, Taylor Perison, Rommie Elizabeth Amaro
POVME 3.0: Software for Mapping Binding Pocket Flexibility. Journal of chemical theory and computation 13 (9) (2017)
Lane William Votapka, Benjamin R Jagger, Alexandra L Heyneman, Rommie Elizabeth Amaro
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding. The journal of physical chemistry. B 121 (15) (2017)