Jerry M Parks (Jerry Parks, J M Parks)

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 45

Top Venues

Nature communications

ACS infectious diseases

Environmental science & technology

The journal of physical chemistry. A

Oak Ridge National Laboratory

Duke University Graduate School (PHD)

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

Affiliation History

Oak Ridge National Laboratory Apr 01 2020

United States

Group Leader, Molecular Biophysics :: Biosciences Division

Oak Ridge National Laboratory

United States

R & D Associate :: Biosciences Division

Oak Ridge National Laboratory

United States

Postdoctoral Research Associate :: Biosciences Division

Education History

Duke University Graduate School

United States

PHD :: Chemistry

Southern Methodist University

United States

MSC :: Department of Chemistry

Texas Christian University

United States

BSC :: Department of Chemistry

Publications

Brian C Sanders, Suman Pokhrel, Audrey D Labbe, Irimpan I Mathews, Connor J Cooper, Russell B Davidson, Gwyndalyn Phillips, Kevin L Weiss, Qiu Zhang, Hugh Michael O'Neill, Manat Kaur, Jurgen G Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W Moriarty, Paul D Adams, Andrzej Joachimiak, Brett L Hurst, Suresh Kumar, Tauseef R Butt, Colleen Beth Jonsson, Lori Ferrins, Soichi Wakatsuki, Stephanie Galanie, Martha S Head, Jerry M Parks
Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature communications 14 (1) (2023)
Benjamin Russell Lewis, Muhammad R Uddin, Mohammad Moniruzzaman, Katie M Kuo, Anna J Higgins, Laila M N Shah, Frank Sobott, Jerry M Parks, Dietmar Hammerschmid, James C Gumbart, Helen I Zgurskaya, Eamonn Reading
Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein. Nature communications 14 (1) (2023)
Brian C Sanders, Suman Pokhrel, Audrey D Labbe, Irimpan I Mathews, Connor J Cooper, Russell B Davidson, Gwyndalyn Phillips, Kevin L Weiss, Qiu Zhang, Hugh Michael O'Neill, Manat Kaur, Jurgen G Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W Moriarty, Paul D Adams, Andrzej Joachimiak, Brett L Hurst, Suresh Kumar, Tauseef R Butt, Colleen Beth Jonsson, Lori Ferrins, Soichi Wakatsuki, Stephanie Galanie, Martha S Head, Jerry M Parks
Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature communications 14 (1) (2023)
Caitlin M Gionfriddo, Ally Bullock Soren, Ann M Wymore, D Sean Hartnett, Mircea Podar, Jerry M Parks, Dwayne A Elias, Cynthia C Gilmour
Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132. Applied and environmental microbiology (2023)
Victoria N Drago, Steven Dajnowicz, Jerry M Parks, Matthew P Blakeley, David A Keen, Nicolas Coquelle, Kevin L Weiss, Oksana Gerlits, Andrey Y Kovalevsky, Timothy C Mueser
An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction. Chemical science 13 (34) (2022)
Mohammad Moniruzzaman, Connor J Cooper, Muhammad R Uddin, John K Walker, Jerry M Parks, Helen I Zgurskaya
Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors. ACS infectious diseases 8 (10) (2022)
Mu Gao, Davi Nakajima An, Jerry M Parks, Jeffrey Skolnick
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning. Nature communications 13 (1) (2022)
Jens Glaser, Ada Sedova, Stephanie Galanie, Daniel W Kneller, Russell B Davidson, Elvis Maradzike, Sara Del Galdo, Audrey Labbé, Darren J Hsu, Rupesh Agarwal, Dmytro Bykov, Arnold Tharrington, Jerry M Parks, Dayle M A Smith, Isabella Daidone, Leighton Coates, Andrey Kovalevsky, Micholas D Smith
Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS pharmacology & translational science 5 (4) (2022)
Yue Shen, Jerry M Parks, Jeremy C Smith
HLA Class I Supertype Classification Based on Structural Similarity. Journal of immunology (Baltimore, Md. : 1950) (2022)
Debjani Pal, Kuntal De, Carly M Shanks, Kai Feng, Timothy B Yates, Jennifer Morrell-Falvey, Russell B Davidson, Jerry M Parks, Wellington Muchero
Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling. Communications biology 5 (1) (2022)
Russell B Davidson, Jess Woods, T Chad Effler, Mathialakan Thavappiragasam, Julie C Mitchell, Jerry M Parks, Ada Sedova
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. Bioinformatics (Oxford, England) 38 (12) (2022)
Brian C Sanders, Suman Pokhrel, Audrey Labbe, Irimpan Mathews, Connor Cooper, Russell Davidson, Gwyndalyn Phillips, Kevin L Weiss, Qiu Zhang, Hugh Michael O'Neill, Manat Kaur, Lori Ferrins, Jurgen G Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W Moriarty, Paul D Adams, Andrzej Joachimiak, Brett L Hurst, Suresh Kumar, Tauseef Butt, Colleen Jonsson, Soichi Wakatsuki, Stephanie Galanie, Martha Head, Jerry M Parks
Potent and Selective Covalent Inhibition of the Papain-like Protease from SARS-CoV-2. Research square (2022)
Brian Sanders, Suman Pohkrel, Audrey Labbe, Irimpan Mathews, Connor Cooper, Russell Davidson, Gwyndalyn Phillips, Kevin L Weiss, Qiu Zhang, Hugh Michael O'Neill, Manat Kaur, Lori Ferrins, Jurgen Schmidt, Walter Reichard, Surekha Surendranathan, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W Moriarty, Paul D Adams, Andrzej Joachimiak, Colleen Jonsson, Soichi Wakatsuki, Stephanie Galanie, Martha Head, Jerry M Parks
Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2. Research square (2021)
Anna Pavlova, Zijian Zhang, Atanu Acharya, Diane L Lynch, Yui Tik Pang, Zhongyu Mou, Jerry M Parks, Christophe J Chipot, James C Gumbart
Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. The journal of physical chemistry letters 12 (23) (2021)
Peng Lian, Zhongyu Mou, Connor J Cooper, Ryne C Johnston, Scott C Brooks, Baohua Gu, Niranjan Govind, Sofi Jonsson, Jerry M Parks
Mechanistic Investigation of Dimethylmercury Formation Mediated by a Sulfide Mineral Surface. The journal of physical chemistry. A 125 (24) (2021)
Helen I Zgurskaya, John K Walker, Jerry M Parks, Valentin V Rybenkov
Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors. Accounts of chemical research 54 (4) (2021)
Reham Ajina, Zoe X Malchiodi, Allison A Fitzgerald, Annie Zuo, Shangzi Wang, Maha Moussa, Connor J Cooper, Yue Shen, Quentin R Johnson, Jerry M Parks, Jeremy C Smith, Marta Catalfamo, Elana J Fertig, Sandra A Jablonski, Louis M Weiner
Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance. Cancer immunology research 9 (4) (2021)
Napoleon D'Cunha, Mohammad Moniruzzaman, Keith Haynes, Giuliano Malloci, Connor J Cooper, Enrico Margiotta, Attilio Vittorio Vargiu, Muhammad R Uddin, Inga V Leus, Feng Cao, Jerry M Parks, Valentin V Rybenkov, Paolo Ruggerone, Helen I Zgurskaya, John K Walker
Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides. ACS infectious diseases 7 (9) (2021)
Sambit K Mishra, Connor J Cooper, Jerry M Parks, Julie C Mitchell
Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes. The journal of physical chemistry. B 125 (23) (2021)
Anna Pavlova, Diane L Lynch, Isabella Daidone, Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot, Daniel W Kneller, Andrey Y Kovalevsky, Leighton Coates, Andrei A Golosov, Callum J Dickson, Camilo Velez-Vega, José S Duca, Josh Vincent Vermaas, Yui Tik Pang, Atanu Acharya, Jerry M Parks, Jeremy C Smith, James C Gumbart
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chemical science 12 (4) (2020)
Deepa Devarajan, Liyuan Liang, Baohua Gu, Scott C Brooks, Jerry M Parks, Micholas D Smith
Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter. Environmental science & technology 54 (21) (2020)
Connor J Cooper, Kaiyuan Zheng, Katherine W Rush, Alexander Johs, Brian C Sanders, Georgios A Pavlopoulos, Nikos C Kyrpides, Mircea Podar, Sergey Ovchinnikov, Stephen W Ragsdale, Jerry M Parks
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation. Communications biology 3 (1) (2020)
Toyokazu Ishida, Jerry M Parks, Micholas D Smith
Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. Journal of the American Chemical Society 142 (42) (2020)
Jerry M Parks, Jeremy C Smith
How to Discover Antiviral Drugs Quickly. The New England journal of medicine 382 (23) (2020)
Kelsi M Sandoz, Roger A Moore, Paul A Beare, Ankur V Patel, Robert E Smith, Marshall Bern, Hyea Hwang, Connor J Cooper, Suzette A Priola, Jerry M Parks, James C Gumbart, Stéphane Mesnage, Robert A Heinzen
β-Barrel proteins tether the outer membrane in many Gram-negative bacteria. Nature microbiology 6 (1) (2020)
Zhongyu Mou, Jason Eakes, Connor J Cooper, Carmen M Foster, Robert F Standaert, Mircea Podar, Mitchel J Doktycz, Jerry M Parks
Machine learning-based prediction of enzyme substrate scope: Application to bacterial nitrilases. Proteins 89 (3) (2020)
Michelle P Aranha, Yead S M Jewel, Robert A Beckman, Louis M Weiner, Julie C Mitchell, Jerry M Parks, Jeremy C Smith
Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions. Journal of immunology (Baltimore, Md. : 1950) 205 (7) (2020)
Atanu Acharya, Rupesh Agarwal, M B Baker, Jerome Y Baudry, Debsindhu Bhowmik, S Boehm, K G Byler, S Y Chen, Leighton Coates, Connor J Cooper, O Demerdash, Isabella Daidone, J D Eblen, S Ellingson, Stefano Forli, J Glaser, James C Gumbart, J Gunnels, O Hernandez, Stephan Irle, D W Kneller, Andrey Y Kovalevsky, J Larkin, T J Lawrence, S LeGrand, Shih-Hsien Liu, J C Mitchell, G Park, Jerry M Parks, A Pavlova, Loukas Petridis, D Poole, L Pouchard, A Ramanathan, David M Rogers, D Santos-Martins, A Scheinberg, Ada Sedova, Y Shen, Micholas D Smith, Micholas Dean Smith, C Soto, A Tsaris, M Thavappiragasam, A F Tillack, Josh Vincent Vermaas, V Q Vuong, J Yin, S Yoo, M Zahran, Laura Zanetti-Polzi
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. Journal of chemical information and modeling 60 (12) (2020)
Xiaohu Hu, Micholas Dean Smith, Bailey M Humphreys, Adam T Green, Jerry M Parks, Jerome Y Baudry, Micholas D Smith
Ligand-Dependent Sodium Ion Dynamics within the A2A Adenosine Receptor: A Molecular Dynamics Study. The journal of physical chemistry. B 123 (38) (2019)
Abu Asaduzzaman, Demian Riccardi, Akef T Afaneh, Connor J Cooper, Micholas D Smith, Feiyue Wang, Jerry M Parks, Georg Schreckenbach
Environmental Mercury Chemistry - In Silico. Accounts of chemical research 52 (2) (2019)
Dan M Close, Connor J Cooper, Xingyou Wang, Payal Chirania, Madhulika Gupta, John R Ossyra, Richard J Giannone, Nancy Engle, Timothy J Tschaplinski, Jeremy C Smith, Lizbeth Hedstrom, Jerry M Parks, Joshua K Michener
Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Molecular microbiology 112 (6) (2019)
Peng Lian, Luanjing Guo, Deepa Devarajan, Jerry M Parks, Scott L Painter, Scott C Brooks, Micholas D Smith
The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. Journal of computational chemistry 41 (2) (2019)
Anthony J Hazel, Narges Abdali, Inga V Leus, Jerry M Parks, Micholas D Smith, Helen I Zgurskaya, James C Gumbart
Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly. ACS infectious diseases 5 (11) (2019)
Swapneeta S Date, Jerry M Parks, Katherine W Rush, Judy D Wall, Stephen W Ragsdale, Alexander Johs
Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB. Applied and environmental microbiology 85 (13) (2019)
Karissa L Cross, James H Campbell, Manasi Balachandran, Alisha G Campbell, Connor J Cooper, Ann Griffen, Matthew Heaton, Snehal Joshi, Dawn Klingeman, Eugene Leys, Zamin Yang, Jerry M Parks, Mircea Podar
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nature biotechnology 37 (11) (2019)
Jing An, Lijie Zhang, Xia Lu, Dale A Pelletier, Eric M Pierce, Alexander Johs, Jerry M Parks, Baohua Gu
Mercury Uptake by Desulfovibrio desulfuricans ND132: Passive or Active? Environmental science & technology 53 (11) (2019)
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. Journal of computational chemistry 41 (6) (2019)
Anna Pavlova, Jerry M Parks, James C Gumbart
Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. Journal of chemical theory and computation 14 (2) (2018)
Connor J Cooper, Ganesh Krishnamoorthy, David Wolloscheck, John K Walker, Valentin V Rybenkov, Jerry M Parks, Helen I Zgurskaya
Molecular Properties That Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa. ACS infectious diseases 4 (8) (2018)
Peng Lian, Ryne C Johnston, Jerry M Parks, Jeremy C Smith
Quantum Chemical Calculation of p Kas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution. The journal of physical chemistry. A 122 (17) (2018)
Jing Zhou, Micholas Dean Smith, Connor J Cooper, Xiaolin Cheng, Jeremy C Smith, Jerry M Parks
Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane. Environmental science & technology 51 (18) (2017)
Keith M Haynes, Narges Abdali, Varsha Jhawar, Helen I Zgurskaya, Jerry M Parks, Adam T Green, Jerome Baudry, Valentin V Rybenkov, Jeremy C Smith, John K Walker
Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. Journal of medicinal chemistry 60 (14) (2017)
Anna Pavlova, Jerry M Parks, Adegboyega K Oyelere, James C Gumbart
Toward the rational design of macrolide antibiotics to combat resistance. Chemical biology & drug design 90 (5) (2017)
Steven Dajnowicz, Ryne C Johnston, Jerry M Parks, Matthew P Blakeley, David A Keen, Kevin L Weiss, Oksana Gerlits, Andrey Y Kovalevsky, Timothy C Mueser
Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nature communications 8 (1) (2017)
Venu Gopal Vandavasi, Patricia S Langan, Kevin L Weiss, Jerry M Parks, Jonathan B Cooper, Stephan L Ginell, Leighton Coates
Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A β-Lactamase with a Monobactam Substrate. Antimicrobial agents and chemotherapy 61 (1) (2016)

Jerry M Parks.css-eqlu8i{font-size:small;padding-left:4px;} (Jerry Parks, J M Parks)

Publication Activity (10 Years)

Top Topics

Top Venues

Jerry M Parks (Jerry Parks, J M Parks)