| Year |
Citation |
Score |
| 2023 |
Davidson RB, Coletti M, Gao M, Piatkowski B, Sreedasyam A, Quadir F, Weston DJ, Schmutz J, Cheng J, Skolnick J, Parks JM, Sedova A. Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. Bioinformatics (Oxford, England). PMID 37589594 DOI: 10.1093/bioinformatics/btad511 |
0.669 |
|
| 2023 |
Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, ... ... Parks JM, et al. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature Communications. 14: 1733. PMID 36977673 DOI: 10.1038/s41467-023-37254-w |
0.701 |
|
| 2022 |
Sanders B, Pokhrel S, Labbe A, Mathews I, Cooper C, Davidson R, Phillips G, Weiss K, Zhang Q, O'Neill H, Kaur M, Ferrins L, Schmidt J, Reichard W, Surendranathan S, ... ... Parks J, et al. Potent and Selective Covalent Inhibition of the Papain-like Protease from SARS-CoV-2. Research Square. PMID 35898342 DOI: 10.21203/rs.3.rs-1840200/v1 |
0.702 |
|
| 2022 |
Pal D, De K, Shanks CM, Feng K, Yates TB, Morrell-Falvey J, Davidson RB, Parks JM, Muchero W. Core cysteine residues in the Plasminogen-Apple-Nematode (PAN) domain are critical for HGF/c-MET signaling. Communications Biology. 5: 646. PMID 35778602 DOI: 10.1038/s42003-022-03582-8 |
0.664 |
|
| 2022 |
Davidson R, Woods J, Effler TC, Thavappiragasam M, Mitchell JC, Parks JM, Sedova A. OpenMDlr: Parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. Bioinformatics (Oxford, England). PMID 35512391 DOI: 10.1093/bioinformatics/btac307 |
0.675 |
|
| 2022 |
Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington A, Parks JM, Smith DMA, Daidone I, et al. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. Acs Pharmacology & Translational Science. 5: 255-265. PMID 35434531 DOI: 10.1021/acsptsci.2c00026 |
0.707 |
|
| 2021 |
Sanders B, Pohkrel S, Labbe A, Mathews I, Cooper C, Davidson R, Phillips G, Weiss K, Zhang Q, O'Neill H, Kaur M, Ferrins L, Schmidt J, Reichard W, Surendranathan S, ... ... Parks J, et al. Potent and Selective Covalent Inhibitors of the Papain-like Protease from SARS-CoV-2. Research Square. PMID 34642689 DOI: 10.21203/rs.3.rs-906621/v1 |
0.672 |
|
| 2020 |
Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion based on a Neutron Structure. Journal of the American Chemical Society. PMID 32959658 DOI: 10.1021/Jacs.0C02148 |
0.355 |
|
| 2020 |
Green AT, Moniruzzaman M, Cooper CJ, Walker JK, Smith JC, Parks JM, Zgurskaya HI. Discovery of multidrug efflux pump inhibitors with a novel chemical scaffold. Biochimica Et Biophysica Acta. General Subjects. 129546. PMID 32032658 DOI: 10.1016/J.Bbagen.2020.129546 |
0.328 |
|
| 2019 |
Hwang H, Hazel A, Lian P, Smith JC, Gumbart JC, Parks JM. A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. Journal of Computational Chemistry. PMID 31721253 DOI: 10.1002/Jcc.26098 |
0.323 |
|
| 2019 |
Close DM, Cooper CJ, Wang X, Chirania P, Gupta M, Ossyra JR, Giannone RJ, Engle N, Tschaplinski TJ, Smith JC, Hedstrom L, Parks JM, Michener JK. Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis. Molecular Microbiology. PMID 31532038 DOI: 10.1111/Mmi.14393 |
0.323 |
|
| 2019 |
Hazel A, Abdali N, Leus I, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational dynamics of AcrA govern multidrug efflux pump assembly. Acs Infectious Diseases. PMID 31517484 DOI: 10.1021/Acsinfecdis.9B00273 |
0.309 |
|
| 2019 |
Darzynkiewicz ZM, Green AT, Abdali N, Hazel A, Fulton RL, Kimball J, Gryczynski Z, Gumbart JC, Parks JM, Smith JC, Zgurskaya HI. Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. Biophysical Journal. PMID 30691677 DOI: 10.1016/J.Bpj.2019.01.010 |
0.315 |
|
| 2019 |
Asaduzzaman A, Riccardi D, Afaneh AT, Cooper SJ, Smith JC, Wang F, Parks JM, Schreckenbach G. Environmental Mercury Chemistry - In Silico. Accounts of Chemical Research. PMID 30689347 DOI: 10.1021/Acs.Accounts.8B00454 |
0.329 |
|
| 2018 |
Kanzler CR, Lian P, Trainer EL, Yang X, Govind N, Parks JM, Graham AM. Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions. Environmental Science. Processes & Impacts. PMID 29388993 DOI: 10.1039/C7Em00533D |
0.304 |
|
| 2018 |
Goins CM, Dajnowicz S, Smith MD, Parks JM, Ronning DR. Mycolyltransferase from Mycobacterium tuberculosis in covalent complex with tetrahydrolipstatin provides insights into Antigen 85 catalysis. The Journal of Biological Chemistry. PMID 29352107 DOI: 10.1074/Jbc.Ra117.001681 |
0.337 |
|
| 2018 |
Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-compatible force-field parameters for cobalamin and related cofactors from quantum mechanical calculations. Journal of Chemical Theory and Computation. PMID 29334459 DOI: 10.1021/Acs.Jctc.7B01236 |
0.341 |
|
| 2018 |
Devarajan D, Lian P, Brooks SC, Parks JM, Smith JC. Quantum Chemical Approach for Calculating Stability Constants of Mercury Complexes Acs Earth and Space Chemistry. 2: 1168-1178. DOI: 10.1021/Acsearthspacechem.8B00102 |
0.306 |
|
| 2018 |
Dajnowicz S, Parks JM, Hu X, Johnston RC, Kovalevsky AY, Mueser TC. Hyperconjugation Promotes Catalysis in a Pyridoxal 5′-Phosphate-Dependent Enzyme Acs Catalysis. 8: 6733-6737. DOI: 10.1021/Acscatal.8B01911 |
0.308 |
|
| 2018 |
Langan PS, Vandavasi VG, Cooper SJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis Acs Catalysis. 8: 2428-2437. DOI: 10.1021/Acscatal.7B04114 |
0.313 |
|
| 2017 |
Dajnowicz S, Johnston RC, Parks JM, Blakeley MP, Keen DA, Weiss KL, Gerlits O, Kovalevsky A, Mueser TC. Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme. Nature Communications. 8: 955. PMID 29038582 DOI: 10.1038/S41467-017-01060-Y |
0.325 |
|
| 2017 |
Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry JY, Rybenkov VV, Smith JC, Walker JK. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. Journal of Medicinal Chemistry. PMID 28650638 DOI: 10.1021/Acs.Jmedchem.7B00453 |
0.335 |
|
| 2017 |
Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Toward the rational design of macrolide antibiotics to combat resistance. Chemical Biology & Drug Design. PMID 28419786 DOI: 10.1111/Cbdd.13004 |
0.301 |
|
| 2017 |
Goins CM, Dajnowicz SJ, Thanna S, Sucheck SJ, Parks JM, Ronning DR. Exploring Covalent Allosteric Inhibition of Antigen 85C from Mycobacterium tuberculosis by Ebselen Derivatives. Acs Infectious Diseases. PMID 28285521 DOI: 10.1021/Acsinfecdis.7B00003 |
0.42 |
|
| 2017 |
Dajnowicz S, Parks JM, Hu X, Gesler K, Kovalevsky AY, Mueser TC. Direct Evidence That an Extended Hydrogen Bonding Network Influences Activation of Pyridoxal 5'-Phosphate in Aspartate Aminotransferase. The Journal of Biological Chemistry. PMID 28232482 DOI: 10.1074/Jbc.M116.774588 |
0.313 |
|
| 2016 |
Abdali N, Parks JM, Haynes K, Chaney JL, Green AT, Wolloscheck D, Walker JK, Rybenkov VV, Baudry JY, Smith JC, Zgurskaya HI. Reviving antibiotics: efflux pump inhibitors that interact with AcrA, a membrane fusion protein of the AcrAB-TolC multidrug efflux pump. Acs Infectious Diseases. PMID 27768847 DOI: 10.1021/Acsinfecdis.6B00167 |
0.302 |
|
| 2016 |
Parks JM, Smith JC. Modeling Mercury in Proteins. Methods in Enzymology. 578: 103-22. PMID 27497164 DOI: 10.1016/Bs.Mie.2016.05.041 |
0.365 |
|
| 2016 |
Gerlits O, Wymore T, Das A, Shen CH, Parks JM, Smith JC, Weiss KL, Keen DA, Blakeley MP, Louis JM, Langan P, Weber IT, Kovalevsky A. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site. Angewandte Chemie (International Ed. in English). PMID 26958828 DOI: 10.1002/Anie.201509989 |
0.316 |
|
| 2015 |
Das A, Gerlits O, Parks JM, Langan P, Kovalevsky A, Heller WT. Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation. Structure (London, England : 1993). PMID 26585512 DOI: 10.1016/J.Str.2015.10.005 |
0.32 |
|
| 2015 |
Wan Q, Parks JM, Hanson BL, Fisher SZ, Ostermann A, Schrader TE, Graham DE, Coates L, Langan P, Kovalevsky A. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proceedings of the National Academy of Sciences of the United States of America. PMID 26392527 DOI: 10.1073/Pnas.1504986112 |
0.314 |
|
| 2014 |
Lian P, Guo HB, Riccardi D, Dong A, Parks JM, Xu Q, Pai EF, Miller SM, Wei DQ, Smith JC, Guo H. 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. Biochemistry. 53: 7211-22. PMID 25343681 DOI: 10.1021/Bi500608U |
0.323 |
|
| 2014 |
Hong L, Sharp MA, Poblete S, Biehl R, Zamponi M, Szekely N, Appavou MS, Winkler RG, Nauss RE, Johs A, Parks JM, Yi Z, Cheng X, Liang L, Ohl M, et al. Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophysical Journal. 107: 393-400. PMID 25028881 DOI: 10.1016/J.Bpj.2014.06.013 |
0.332 |
|
| 2014 |
Wymore T, Field MJ, Langan P, Smith JC, Parks JM. Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: implications for engineering bioscavengers. The Journal of Physical Chemistry. B. 118: 4479-89. PMID 24720808 DOI: 10.1021/Jp410422C |
0.338 |
|
| 2014 |
Zhou J, Riccardi D, Beste A, Smith JC, Parks JM. Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II). Inorganic Chemistry. 53: 772-7. PMID 24377658 DOI: 10.1021/Ic401992Y |
0.305 |
|
| 2014 |
Kovalevsky A, Wymore T, Sangha A, Challacombe M, Mason S, Forsyth T, Parks J, Keen D, Graham D, Langan P. Combining neutron crystallography, high-performance computing for enzyme design Acta Crystallographica Section a Foundations and Advances. 70: C1204-C1204. DOI: 10.1107/S2053273314087956 |
0.343 |
|
| 2013 |
Chaudret R, Parks JM, Yang W. Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs. The Journal of Chemical Physics. 138: 045102. PMID 23387624 DOI: 10.1063/1.4772182 |
0.721 |
|
| 2013 |
Riccardi D, Guo HB, Parks JM, Gu B, Summers AO, Miller SM, Liang L, Smith JC. Why mercury prefers soft ligands Journal of Physical Chemistry Letters. 4: 2317-2322. DOI: 10.1021/Jz401075B |
0.31 |
|
| 2012 |
Mintz BJ, Parks JM. Benchmark interaction energies for biologically relevant noncovalent complexes containing divalent sulfur. The Journal of Physical Chemistry. A. 116: 1086-92. PMID 22181988 DOI: 10.1021/Jp209536E |
0.306 |
|
| 2012 |
Sangha AK, Petridis L, Smith JC, Ziebell A, Parks JM. Molecular simulation as a tool for studying lignin Environmental Progress and Sustainable Energy. 31: 47-54. DOI: 10.1002/Ep.10628 |
0.306 |
|
| 2011 |
Johs A, Harwood IM, Parks JM, Nauss RE, Smith JC, Liang L, Miller SM. Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase. Journal of Molecular Biology. 413: 639-56. PMID 21893070 DOI: 10.1016/J.Jmb.2011.08.042 |
0.342 |
|
| 2011 |
Johs A, Parks JM, Harwood I, Guo H, Smith J, Miller SM, Summers AO, Liang L. Biomolecular Mechanisms of Microbial Mercury Resistance in the Environment Biophysical Journal. 100: 313a. DOI: 10.1016/J.Bpj.2010.12.1910 |
0.342 |
|
| 2010 |
Guo HB, Johs A, Parks JM, Olliff L, Miller SM, Summers AO, Liang L, Smith JC. Structure and conformational dynamics of the metalloregulator MerR upon binding of Hg(II). Journal of Molecular Biology. 398: 555-68. PMID 20303978 DOI: 10.1016/J.Jmb.2010.03.020 |
0.316 |
|
| 2009 |
Parks JM, Guo H, Momany C, Liang L, Miller SM, Summers AO, Smith JC. Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. Journal of the American Chemical Society. 131: 13278-85. PMID 19719173 DOI: 10.1021/Ja9016123 |
0.353 |
|
| 2009 |
Parks JM, Hu H, Rudolph J, Yang W. Mechanism of Cdc25B phosphatase with the small molecule substrate p-nitrophenyl phosphate from QM/MM-MFEP calculations. The Journal of Physical Chemistry. B. 113: 5217-24. PMID 19301836 DOI: 10.1021/Jp805137X |
0.549 |
|
| 2008 |
Parks JM, Hu H, Cohen AJ, Yang W. A pseudobond parametrization for improved electrostatics in quantum mechanical/molecular mechanical simulations of enzymes. The Journal of Chemical Physics. 129: 154106. PMID 19045175 DOI: 10.1063/1.2994288 |
0.509 |
|
| 2008 |
Parks JM, Kondru RK, Hu H, Beratan DN, Yang W. Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding. The Journal of Physical Chemistry. B. 112: 3168-76. PMID 18271573 DOI: 10.1021/Jp076885J |
0.5 |
|
| 2008 |
Hu H, Lu Z, Parks JM, Burger SK, Yang W. 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. The Journal of Chemical Physics. 128: 034105. PMID 18205486 DOI: 10.1063/1.2816557 |
0.715 |
|
| 2005 |
Sohn J, Parks JM, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner H, Yang W, Rudolph J. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44: 16563-73. PMID 16342947 DOI: 10.1021/Bi0516879 |
0.542 |
|
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