Jerry M. Parks

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Hotspot coevolution at protein-protein interfaces is a key identifier of native protein complexes

Julie C. Mitchell, Sambit Mishra, Sarah J. Cooper, 2019, bioRxiv.

HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

Jeremy C. Smith, Jerry M. Parks, Demian Riccardi, 2015, J. Chem. Inf. Model..

Author response for "Machine Learning‐based Prediction of Enzyme Substrate Scope: Application to Bacterial Nitrilases"

Robert F. Standaert, Jerry M. Parks, Carmen M. Foster, 2020 .

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Ada Sedova, Mathialakan Thavappiragasam, Jerry M. Parks, 2021, BCB.

X-ray Structure of a Hg2+ Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg2+ Transfer between the C-Terminal and Buried Catalytic Site Cysteine Pairs

Dong-Qing Wei, Hao-Bo Guo, Jerry M. Parks, 2014, Biochemistry.

Quantum Chemical Approach for Calculating Stability Constants of Mercury Complexes

Scott C. Brooks, Deepa Devarajan, Jerry M. Parks, 2018, ACS Earth and Space Chemistry.

Quantum Chemical Calculation of p Kas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines, and Thiols in Aqueous Solution.

Jerry M. Parks, Peng Lian, Jeremy C. Smith, 2018, The journal of physical chemistry. A.

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

Jerry M. Parks, J. Skolnick, M. Gao, 2022, Nature Communications.

Transcriptional control of hgcAB by an ArsR-like regulator in Pseudodesulfovibrio mercurii ND132

Jerry M. Parks, C. Gilmour, M. Podar, 2022, bioRxiv.

Plant Cell Walls: Basics of Structure, Chemistry, Accessibility and the Influence on Conversion

Mark F. Davis, Jerry M. Parks, B. Davison, 2013 .

Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB

Jerry M. Parks, S. Ragsdale, J. Parks, 2019, Applied and Environmental Microbiology.

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

Jerry M. Parks, M. Podar, James H. Campbell, 2019, Nature Biotechnology.

HLA-Clus: HLA class I clustering based on 3D structure

Jerry M. Parks, J. Parks, Jeremy C. Smith, 2023, BMC Bioinformatics.

Exceptional response and multisystem autoimmune-like toxicities associated with the same T cell clone in a patient with uveal melanoma treated with immune checkpoint inhibitors

Sarah J. Cooper, Jerry M. Parks, P. Sorger, 2019, Journal of Immunotherapy for Cancer.

Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, bioRxiv.

Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease

Jerry M. Parks, Jeremy C. Smith, Callum J. Dickson, 2020, bioRxiv.

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog

Jerry M. Parks, Jeremy C. Smith, R. Dixon, 2012, Biotechnology for Biofuels.

Impact of hydration and temperature history on the structure and dynamics of lignin

Jerry M. Parks, Jeremy C. Smith, A. Ragauskas, 2018 .

The Genetic Basis for Bacterial Mercury Methylation

Jerry M. Parks, Jeremy C. Smith, Jeremy C Smith, 2013, Science.

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Georgios A. Pavlopoulos, Jerry M. Parks, N. Kyrpides, 2020, Communications Biology.

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Jerry M. Parks, N. Kyrpides, S. Ovchinnikov, 2020, Communications Biology.

The AQUA‐MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation

Jerry M. Parks, Peng Lian, Jeremy C. Smith, 2020, J. Comput. Chem..

A probabilistic perspective on thermodynamic parameter uncertainties: Understanding aqueous speciation of mercury

Jerry M. Parks, Jeremy C. Smith, S. Brooks, 2019, Geochimica et Cosmochimica Acta.

Mercury Uptake by Desulfovibrio desulfuricans ND132: Passive or Active?

Jerry M. Parks, J. Parks, A. Johs, 2019, Environmental science & technology.

Environmental Mercury Chemistry - In Silico.

Sarah J. Cooper, Jerry M. Parks, Jeremy C. Smith, 2019, Accounts of chemical research.

Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes

Jerry M. Parks, R. Hettich, J. Parks, 2018, Proteomics.

Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions.

Niranjan Govind, Jerry M. Parks, Peng Lian, 2018, Environmental science. Processes & impacts.

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

Jerry M. Parks, J. Gumbart, J. Parks, 2018, Journal of chemical theory and computation.

Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

Jerry M. Parks, Jeremy C. Smith, J. Parks, 2016, The journal of physical chemistry. B.

Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation

Jerry M. Parks, M. Podar, J. Parks, 2015, Applied and Environmental Microbiology.

Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II).

Jerry M. Parks, Jeremy C. Smith, Jeremy C Smith, 2014, Inorganic chemistry.

Why Mercury Prefers Soft Ligands

Jerry M. Parks, Jeremy C. Smith, D. Riccardi, 2013 .

Modeling Mercury in Proteins.

Jerry M. Parks, Jeremy C. Smith, J. Parks, 2016, Methods in enzymology.

Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II).

Jerry M. Parks, Jeremy C. Smith, A. Johs, 2010, Journal of molecular biology.

Direct visualization of critical hydrogen atoms in a pyridoxal 5′-phosphate enzyme

Jerry M. Parks, S. Dajnowicz, J. Parks, 2017, Nature Communications.

Direct evidence that an extended hydrogen-bonding network influences activation of pyridoxal 5′-phosphate in aspartate aminotransferase

Jerry M. Parks, S. Dajnowicz, J. Parks, 2017, The Journal of Biological Chemistry.

Machine learning‐based prediction of enzyme substrate scope: Application to bacterial nitrilases

Jerry M. Parks, M. Podar, J. Parks, 2020, Proteins.

Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase.

Jerry M. Parks, Jeremy C. Smith, Jeremy C Smith, 2011, Journal of molecular biology.

L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.

Jerry M. Parks, Jeremy C. Smith, H. L. Carrell, 2014, Structure.

Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold.

Jerry M. Parks, Jeremy C. Smith, M. Moniruzzaman, 2020, Biochimica et biophysica acta. General subjects.

Reviving Antibiotics: Efflux Pump Inhibitors That Interact with AcrA, a Membrane Fusion Protein of the AcrAB-TolC Multidrug Efflux Pump.

Julie L. Chaney, Jerry M. Parks, A. T. Green, 2017, ACS infectious diseases.

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, Biophysical Journal.

Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum

Jerry M. Parks, Jeremy C. Smith, Shihui Yang, 2011, Proceedings of the National Academy of Sciences.

Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase.

Jerry M. Parks, Jeremy C. Smith, R. Winkler, 2014, Biophysical journal.

Analysis of Orthogonal Efflux and Permeation Properties of Compounds Leads to the Discovery of New Efflux Pump Inhibitors.

Jerry M. Parks, M. Moniruzzaman, J. Parks, 2022, ACS infectious diseases.

Comparative informatics analysis to evaluate site-specific protein oxidation in multidimensional LC-MS/MS data.

Jerry M. Parks, R. Hettich, J. Parks, 2013, Journal of proteome research.

Hydrolysis of DFP and the Nerve Agent (S)-Sarin by DFPase Proceeds along Two Different Reaction Pathways: Implications for Engineering Bioscavengers

Jerry M. Parks, Jeremy C. Smith, M. Field, 2014, The journal of physical chemistry. B.

Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling

Jerry M. Parks, Russell B. Davidson, J. Morrell-Falvey, 2022, Communications Biology.

Core cysteine residues in the PAN domain are critical for HGF/c-MET signaling

Jerry M. Parks, Russell B. Davidson, J. Morrell-Falvey, 2021, bioRxiv.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, Journal of chemical information and modeling.

Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance

Jerry M. Parks, Jeremy C. Smith, Quentin R. Johnson, 2021, Cancer Immunology Research.

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Jerry M. Parks, Steven K. Burger, Weitao Yang, 2008, The Journal of chemical physics.

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

Jerry M. Parks, J. Parks, I. V. Leus, 2022, Scientific Reports.

Molecular Properties That Define the Activities of Antibiotics in Escherichia coli and Pseudomonas aeruginosa.

Sarah J. Cooper, Jerry M. Parks, J. Parks, 2018, ACS infectious diseases.

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Arnold N. Tharrington, Jerry M. Parks, Russell B. Davidson, 2022, ACS pharmacology & translational science.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Duncan Poole, John A. Gunnels, Arvind Ramanathan, 2020, J. Chem. Inf. Model..

Predicting direct physical interactions in multimeric proteins with deep learning

Jerry M. Parks, J. Skolnick, M. Gao, 2021, bioRxiv.

HLA Class I Supertype Classification Based on Structural Similarity.

Jerry M. Parks, J. Parks, Yue Shen, 2022, Journal of immunology.

Conformational dynamics of AcrA govern multidrug efflux pump assembly.

Jerry M. Parks, Jeremy C. Smith, J. Gumbart, 2019, ACS infectious diseases.

Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate.

Jerry M. Parks, H. Edelsbrunner, J. Rudolph, 2005, Biochemistry.

Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis

Jerry M. Parks, C. Goins, S. Dajnowicz, 2018, The Journal of Biological Chemistry.

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide–MHC Binding Predictions

Julie C. Mitchell, Jerry M. Parks, Jeremy C. Smith, 2020, The Journal of Immunology.

Combining 3D modeling with artificial intelligence to increase specificity and precision in peptide:MHC binding predictions

Jerry M. Parks, L. Weiner, J. Parks, 2020 .

Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors.

Jerry M. Parks, J. Parks, H. Zgurskaya, 2021, Accounts of chemical research.

Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations.

Jerry M. Parks, Jeremy C. Smith, D. Riccardi, 2013, Journal of chemical theory and computation.

Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

Jerry M. Parks, Jeremy C. Smith, J. Louis, 2016, Angewandte Chemie.

Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

Joshua K. Michener, Sarah J. Cooper, Jerry M. Parks, 2018, bioRxiv.

High-performance computer simulation in the energy biosciences

Jerry M. Parks, Jeremy C. Smith, B. Lindner, 2011 .

Immune Selection Pressure Contributes to Pancreatic Cancer Immune Evasion

Jerry M. Parks, Jeremy C. Smith, Quentin R. Johnson, 2020, bioRxiv.

Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump.

Jerry M. Parks, Jeremy C. Smith, M. Beeby, 2021, Biophysical journal.

Bacterial Efflux Pumps and Their Inhibitors

Jerry M. Parks, J. Parks, H. Zgurskaya, 2021 .

Distribution of mechanical stress in the Escherichia coli cell envelope.

Jerry M. Parks, J. Gumbart, J. Lakey, 2018, Biochimica et biophysica acta. Biomembranes.

Transcriptional Control of hgcAB by an ArsR-Like Regulator in Pseudodesulfovibrio mercurii ND132

Jerry M. Parks, C. Gilmour, M. Podar, 2023, Applied and environmental microbiology.

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Jerry M. Parks, Russell B. Davidson, J. Skolnick, 2023, Bioinform..

Understanding enzyme catalysis using computer simulation

Jerry M. Parks, Jeremy C. Smith, P. Imhof, 2010 .

Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation.

Jerry M. Parks, P. Langan, J. Parks, 2015, Structure.

Active-Site Protonation States in an Acyl-Enzyme Intermediate of a Class A β-Lactamase with a Monobactam Substrate

Jerry M. Parks, J. Cooper, J. Parks, 2016, Antimicrobial Agents and Chemotherapy.

Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion based on a Neutron Structure.

Jerry M. Parks, Jeremy C. Smith, J. Parks, 2020, Journal of the American Chemical Society.

Mechanism of Hg-C protonolysis in the organomercurial lyase MerB.

Jerry M. Parks, Jeremy C. Smith, J. Parks, 2009, Journal of the American Chemical Society.

Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives.

Jerry M. Parks, C. Goins, S. Dajnowicz, 2017, ACS infectious diseases.

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Jerry M. Parks, Steven K. Burger, Weitao Yang, 2008, Journal of Chemical Physics.

A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes.

Jerry M. Parks, Weitao Yang, A. Cohen, 2008, The Journal of chemical physics.

Mechanistic Duality of Bacterial Efflux Substrates and Inhibitors: Example of Simple Substituted Cinnamoyl and Naphthyl Amides.

Jerry M. Parks, P. Ruggerone, M. Moniruzzaman, 2021, ACS infectious diseases.

Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA.

Jerry M. Parks, A. T. Green, Jeremy C. Smith, 2019, Biophysical journal.

An N⋯H⋯N low-barrier hydrogen bond preorganizes the catalytic site of aspartate aminotransferase to facilitate the second half-reaction

Jerry M. Parks, S. Dajnowicz, J. Parks, 2022, Chemical science.

Toward the rational design of macrolide antibiotics to combat resistance

Jerry M. Parks, J. Gumbart, J. Parks, 2017, Chemical biology & drug design.

Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II).

Jerry M. Parks, Jeremy C. Smith, A. Johs, 2010, Journal of molecular biology.

Modeling of the Passive Permeation of Mercury and Methylmercury Complexes Through a Bacterial Cytoplasmic Membrane.

Sarah J. Cooper, Jerry M. Parks, Jeremy C. Smith, 2017, Environmental science & technology.

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

Jerry M. Parks, R. Heinzen, J. Gumbart, 2020, Nature Microbiology.

β-Barrel Proteins Tether the Outer Membrane in Many Gram-Negative Bacteria

Jerry M. Parks, Ankur V Patel, R. Heinzen, 2020, Nature microbiology.

Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs.

Jerry M. Parks, Weitao Yang, J. Parks, 2013, The Journal of chemical physics.

Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2

Jerry M. Parks, Russell B. Davidson, D. Sterner, 2023, Nature Communications.

Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions.

Jerry M. Parks, N. Govind, P. Lian, 2018, Environmental science. Processes & impacts.

Benchmark interaction energies for biologically relevant noncovalent complexes containing divalent sulfur.

Jerry M. Parks, Benjamin Mintz, 2012, The journal of physical chemistry. A.

Hotspot Coevolution Is a Key Identifier of Near-Native Protein Complexes.

Julie C. Mitchell, Jerry M. Parks, S. Mishra, 2021, The journal of physical chemistry. B.

Molecular simulation as a tool for studying lignin

Jerry M. Parks, Loukas Petridis, J. Parks, 2012 .

Trace: Tennessee Research and Creative Exchange Biochemistry, Cellular and Molecular Biology Publications and Other Works Biochemistry, Cellular and Molecular Biology Down-regulation of the Caffeic Acid O- Methyltransferase Gene in Switchgrass Reveals a Novel Monolignol Analog Recommended Citation D

Jerry M. Parks, Jeremy C. Smith, R. Dixon, 2022 .

Potent and Selective Covalent Inhibition of the Papain-like Protease from SARS-CoV-2

Jerry M. Parks, Russell B. Davidson, M. Head, 2021, Research square.

Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase.

Jerry M. Parks, Jeremy C. Smith, R. Winkler, 2014, Biophysical journal.

Radical coupling reactions in lignin synthesis: a density functional theory study.

Mark F. Davis, Jerry M. Parks, Jeremy C. Smith, 2012, The journal of physical chemistry. B.

L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase: X-ray/neutron crystallographic and molecular simulation study.

Jerry M. Parks, Jeremy C. Smith, H. L. Carrell, 2014, Structure.

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

Jerry M. Parks, A. J. Higgins, M. Moniruzzaman, 2022, bioRxiv.

Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli.

Jerry M. Parks, A. T. Green, Jeremy C. Smith, 2017, Journal of medicinal chemistry.