Works matching AU Parks, Jerry M.

Results: 21

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances.

Published in:

Bioinformatics, 2022, v. 38, n. 12, p. 3297, doi. 10.1093/bioinformatics/btac307

By:

Davidson, Russell B;
Woods, Jess;
Effler, T Chad;
Thavappiragasam, Mathialakan;
Mitchell, Julie C;
Parks, Jerry M;
Sedova, Ada

Publication type:

Article

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

Published in:

Biotechnology for Biofuels, 2012, v. 5, n. 1, p. 71, doi. 10.1186/1754-6834-5-71

By:

Tschaplinski, Timothy J.;
Standaert, Robert F.;
Engle, Nancy L.;
Martin, Madhavi Z.;
Sangha, Amandeep K.;
Parks, Jerry M.;
Smith, Jeremy C.;
Samuel, Reichel;
Nan Jiang;
Yunqiao Pu;
Ragauskas, Arthur J.;
Hamilton, Choo Y.;
Chunxiang Fu;
Zeng-Yu Wang;
Davison, Brian H.;
Dixon, Richard A.;
Mielenz, Jonathan R.

Publication type:

Article

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-39615-x

By:

Russell Lewis, Benjamin;
Uddin, Muhammad R.;
Moniruzzaman, Mohammad;
Kuo, Katie M.;
Higgins, Anna J.;
Shah, Laila M. N.;
Sobott, Frank;
Parks, Jerry M.;
Hammerschmid, Dietmar;
Gumbart, James C.;
Zgurskaya, Helen I.;
Reading, Eamonn

Publication type:

Article

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics.

Published in:

Nature Biotechnology, 2019, v. 37, n. 11, p. 1314, doi. 10.1038/s41587-019-0260-6

By:

Cross, Karissa L.;
Campbell, James H.;
Balachandran, Manasi;
Campbell, Alisha G.;
Cooper, Sarah J.;
Griffen, Ann;
Heaton, Matthew;
Joshi, Snehal;
Klingeman, Dawn;
Leys, Eugene;
Yang, Zamin;
Parks, Jerry M.;
Podar, Mircea

Publication type:

Article

Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-12376-1

By:

Leus, Inga V.;
Weeks, Jon W.;
Bonifay, Vincent;
Shen, Yue;
Yang, Liang;
Cooper, Connor J.;
Nash, Dinesh;
Duerfeldt, Adam S.;
Smith, Jeremy C.;
Parks, Jerry M.;
Rybenkov, Valentin V.;
Zgurskaya, Helen I.

Publication type:

Article

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

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01060-y

By:

Dajnowicz, Steven;
Johnston, Ryne C.;
Parks, Jerry M.;
Blakeley, Matthew P.;
Keen, David A.;
Weiss, Kevin L.;
Gerlits, Oksana;
Kovalevsky, Andrey;
Mueser, Timothy C.

Publication type:

Article

Molecular simulation as a tool for studying lignin.

Published in:

Environmental Progress & Sustainable Energy, 2012, v. 31, n. 1, p. 47, doi. 10.1002/ep.10628

By:

Sangha, Amandeep K.;
Petridis, Loukas;
Smith, Jeremy C.;
Ziebell, Angela;
Parks, Jerry M.

Publication type:

Article

Toward the rational design of macrolide antibiotics to combat resistance.

Published in:

2017

By:

Pavlova, Anna;
Parks, Jerry M.;
Oyelere, Adegboyega K.;
Gumbart, James C.

Publication type:

Editorial

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

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05297-x

By:

Shen, Yue;
Parks, Jerry M.;
Smith, Jeremy C.

Publication type:

Article

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

Published in:

Proteomics, 2018, v. 18, n. 17, p. 1, doi. 10.1002/pmic.201700479

By:

Qian, Chen;
Chen, Hongmei;
Johs, Alexander;
Lu, Xia;
An, Jing;
Pierce, Eric M.;
Parks, Jerry M.;
Elias, Dwayne A.;
Hettich, Robert L.;
Gu, Baohua

Publication type:

Article

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation.

Published in:

Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad511

By:

Davidson, Russell B;
Coletti, Mark;
Gao, Mu;
Piatkowski, Bryan;
Sreedasyam, Avinash;
Quadir, Farhan;
Weston, David J;
Schmutz, Jeremy;
Cheng, Jianlin;
Skolnick, Jeffrey;
Parks, Jerry M;
Sedova, Ada

Publication type:

Article

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

Published in:

Communications Biology, 2022, v. 5, n. 1, p. 1, doi. 10.1038/s42003-022-03582-8

By:

Pal, Debjani;
De, Kuntal;
Shanks, Carly M.;
Feng, Kai;
Yates, Timothy B.;
Morrell-Falvey, Jennifer;
Davidson, Russell B.;
Parks, Jerry M.;
Muchero, Wellington

Publication type:

Article

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.

Published in:

Journal of Computational Chemistry, 2020, v. 41, n. 6, p. 528, doi. 10.1002/jcc.26098

By:

Hwang, Hyea;
Hazel, Anthony;
Lian, Peng;
Smith, Jeremy C.;
Gumbart, James C.;
Parks, Jerry M.

Publication type:

Article

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

Published in:

Journal of Computational Chemistry, 2020, v. 41, n. 2, p. 147, doi. 10.1002/jcc.26081

By:

Lian, Peng;
Guo, Luanjing;
Devarajan, Deepa;
Parks, Jerry M.;
Painter, Scott L.;
Brooks, Scott C.;
Smith, Jeremy C.

Publication type:

Article

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

Published in:

Proteins, 2021, v. 89, n. 3, p. 336, doi. 10.1002/prot.26019

By:

Mou, Zhongyu;
Eakes, Jason;
Cooper, Connor J.;
Foster, Carmen M.;
Standaert, Robert F.;
Podar, Mircea;
Doktycz, Mitchel J.;
Parks, Jerry M.

Publication type:

Article

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

Published in:

Angewandte Chemie International Edition, 2016, v. 55, n. 16, p. 4924, doi. 10.1002/anie.201509989

By:

Gerlits, Oksana;
Wymore, Troy;
Das, Amit;
Shen, Chen-Hsiang;
Parks, Jerry M.;
Smith, Jeremy C.;
Weiss, Kevin L.;
Keen, David A.;
Blakeley, Matthew P.;
Louis, John M.;
Langan, Paul;
Weber, Irene T.;
Kovalevsky, Andrey

Publication type:

Article

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

Published in:

Angewandte Chemie, 2016, v. 128, n. 16, p. 5008, doi. 10.1002/ange.201509989

By:

Gerlits, Oksana;
Wymore, Troy;
Das, Amit;
Shen, Chen ‐ Hsiang;
Parks, Jerry M.;
Smith, Jeremy C.;
Weiss, Kevin L.;
Keen, David A.;
Blakeley, Matthew P.;
Louis, John M.;
Langan, Paul;
Weber, Irene T.;
Kovalevsky, Andrey

Publication type:

Article

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

Published in:

Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-1047-5

By:

Cooper, Connor J.;
Zheng, Kaiyuan;
Rush, Katherine W.;
Johs, Alexander;
Sanders, Brian C.;
Pavlopoulos, Georgios A.;
Kyrpides, Nikos C.;
Podar, Mircea;
Ovchinnikov, Sergey;
Ragsdale, Stephen W.;
Parks, Jerry M.

Publication type:

Article

Author Correction: Property space mapping of Pseudomonas aeruginosa permeability to small molecules.

Published in:

2023

By:

Leus, Inga V.;
Weeks, Jon W.;
Bonifay, Vincent;
Shen, Yue;
Yang, Liang;
Cooper, Connor J.;
Nath, Dinesh;
Duerfeldt, Adam S.;
Smith, Jeremy C.;
Parks, Jerry M.;
Rybenkov, Valentin V.;
Zgurskaya, Helen I.

Publication type:

Correction Notice

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

Published in:

Molecular Microbiology, 2019, v. 112, n. 6, p. 1784, doi. 10.1111/mmi.14393

By:

Close, Dan M.;
Cooper, Connor J.;
Wang, Xingyou;
Chirania, Payal;
Gupta, Madhulika;
Ossyra, John R.;
Giannone, Richard J.;
Engle, Nancy;
Tschaplinski, Timothy J.;
Smith, Jeremy C.;
Hedstrom, Lizbeth;
Parks, Jerry M.;
Michener, Joshua K.

Publication type:

Article

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29394-2

By:

Gao, Mu;
Nakajima An, Davi;
Parks, Jerry M.;
Skolnick, Jeffrey

Publication type:

Article