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

por Shen, Yue, Parks, Jerry M., Smith, Jeremy C.
Publicado 2023

AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

por Gao, Mu, Nakajima An, Davi, Parks, Jerry M., Skolnick, Jeffrey
Publicado 2022

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

por Wymore, Troy, Field, Martin J., Langan, Paul, Smith, Jeremy C., Parks, Jerry M.
Publicado 2014

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

por Vandavasi, Venu Gopal, Langan, Patricia S., Weiss, Kevin L., Parks, Jerry M., Cooper, Jonathan B., Ginell, Stephan L., Coates, Leighton
Publicado 2016

Machine learning reveals the critical interactions for SARS-CoV-2 spike protein binding to ACE2

por Pavlova, Anna, Zhang, Zijian, Acharya, Atanu, Lynch, Diane L., Tik Pang, Yui, Mou, Zhongyu, Parks, Jerry M., Chipot, Christophe J., Gumbart, James C.
Publicado 2022

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

por Pal, Debjani, De, Kuntal, Shanks, Carly M., Feng, Kai, Yates, Timothy B., Morrell-Falvey, Jennifer, Davidson, Russell B., Parks, Jerry M., Muchero, Wellington
Publicado 2022

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

por Dajnowicz, Steven, Johnston, Ryne C., Parks, Jerry M., Blakeley, Matthew P., Keen, David A., Weiss, Kevin L., Gerlits, Oksana, Kovalevsky, Andrey, Mueser, Timothy C.
Publicado 2017

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

por Drago, Victoria N., Dajnowicz, Steven, Parks, Jerry M., Blakeley, Matthew P., Keen, David A., Coquelle, Nicolas, Weiss, Kevin L., Gerlits, Oksana, Kovalevsky, Andrey, Mueser, Timothy C.
Publicado 2022

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

por 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
Publicado 2023

X-ray Structure of a Hg(2+) Complex of Mercuric Reductase (MerA) and Quantum Mechanical/Molecular Mechanical Study of Hg(2+) Transfer between the C-Terminal and Buried Catalytic Si...

por Lian, Peng, Guo, Hao-Bo, Riccardi, Demian, Dong, Aiping, Parks, Jerry M., Xu, Qin, Pai, Emil F., Miller, Susan M., Wei, Dong-Qing, Smith, Jeremy C., Guo, Hong
Publicado 2014

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

por Rapisuwon, Suthee, Izar, Benjamin, Batenchuk, Cory, Avila, Alexandre, Mei, Shaolin, Sorger, Peter, Parks, Jerry M., Cooper, Sarah J., Wagner, David, Zeck, Jay C., Charabaty, Aline J., Atkins, Michael B.
Publicado 2019

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

por 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.
Publicado 2020

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

por 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.
Publicado 2023

Targeted isolation and cultivation of uncultivated bacteria by reverse genomics

por Cross, Karissa L., Campbell, James H., Balachandran, Manasi, Campbell, Alisha G., Cooper, Connor J., Griffen, Ann, Heaton, Matthew, Joshi, Snehal, Klingeman, Dawn, Leys, Eugene, Yang, Zamin, Parks, Jerry M., Podar, Mircea
Publicado 2019

Property space mapping of Pseudomonas aeruginosa permeability to small molecules

por 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.
Publicado 2022

Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein

por 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
Publicado 2023

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

por Sandoz, Kelsi M., Moore, Roger A., Beare, Paul A., Patel, Ankur V., Smith, Robert E., Bern, Marshall, Hwang, Hyea, Cooper, Connor J., Priola, Suzette A., Parks, Jerry M., Gumbart, James C., Mesnage, Stéphane, Heinzen, Robert A.
Publicado 2020

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

por Glaser, Jens, Sedova, Ada, Galanie, Stephanie, Kneller, Daniel W., Davidson, Russell B., Maradzike, Elvis, Del Galdo, Sara, Labbé, Audrey, Hsu, Darren J., Agarwal, Rupesh, Bykov, Dmytro, Tharrington, Arnold, Parks, Jerry M., Smith, Dayle M. A., Daidone, Isabella, Coates, Leighton, Kovalevsky, Andrey, Smith, Jeremy C.
Publicado 2022

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

por Tschaplinski, Timothy J, Standaert, Robert F, Engle, Nancy L, Martin, Madhavi Z, Sangha, Amandeep K, Parks, Jerry M, Smith, Jeremy C, Samuel, Reichel, Jiang, Nan, Pu, Yunqiao, Ragauskas, Arthur J, Hamilton, Choo Y, Fu, Chunxiang, Wang, Zeng-Yu, Davison, Brian H, Dixon, Richard A, Mielenz, Jonathan R
Publicado 2012

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

por Pavlova, Anna, Lynch, Diane L., Daidone, Isabella, Zanetti-Polzi, Laura, Smith, Micholas Dean, Chipot, Chris, Kneller, Daniel W., Kovalevsky, Andrey, Coates, Leighton, Golosov, Andrei A., Dickson, Callum J., Velez-Vega, Camilo, Duca, José S., Vermaas, Josh V., Pang, Yui Tik, Acharya, Atanu, Parks, Jerry M., Smith, Jeremy C., Gumbart, James C.
Publicado 2020