Paul D Adams (P D Adams, Paul Adams)

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 43

Top Venues

Acta crystallographica. Section D, Structural biology

Nature

Nature plants

Nature methods

University of California, Berkeley

University of Edinburgh (PHD)

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

Affiliation History

University of California, Berkeley

United States

Professor :: Bioengineering

Education History

University of Edinburgh

United Kingdom

PHD :: Biochemistry

Publications

Dorothee Liebschner, Pavel V Afonine, Billy K Poon, Nigel W Moriarty, Paul D Adams
Improved joint X-ray and neutron refinement procedure in Phenix. Acta crystallographica. Section D, Structural biology (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)
Jing Huang, Andrew Quest, Pablo Cruz-Morales, Kai Deng, Jose Henrique Pereira, Devon Van Cura, Ramu Kakumanu, Edward E K Baidoo, Qingyun Dan, Yan Chen, Christopher J Petzold, Trent R Northen, Paul D Adams, Douglas S Clark, Emily P Balskus, John F Hartwig, Aindrila Mukhopadhyay, Jay D Keasling
Complete integration of carbene-transfer chemistry into biosynthesis. Nature 617 (7960) (2023)
Dorothee Liebschner, Nigel W Moriarty, Billy K Poon, Paul D Adams
In situ ligand restraints from quantum-mechanical methods. Acta crystallographica. Section D, Structural biology 79 (Pt 2) (2023)
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J Kaminsky, Miao Zhang, Julia Gätcke, Stephanie Haupt, Isabela I Nangca, Stephen M Keable, A Orkun Aydin, Kensure Tono, Shigeki Owada, Leland B Gee, Franklin D Fuller, Alexander Batyuk, Roberto Alonso Mori, James M Holton, Daniel W Paley, Nigel W Moriarty, Fikret Mamedov, Paul D Adams, Aaron S Brewster, Holger Dobbek, Nicholas K Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan F Kern, Junko Yano, Vittal K Yachandra
Structural evidence for intermediates during O 2 formation in photosystem II. Nature (2023)
Pradeep Kumar Prabhakar, Jose Henrique Pereira, Rahil Taujale, Wanchen Shao, Vivek S Bharadwaj, Digantkumar Chapla, Jeong-Yeh Yang, Yannick J Bomble, Kelley W Moremen, Natarajan Kannan, Michal Hammel, Paul D Adams, Henrik Vibe Scheller, Breeanna R Urbanowicz
Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature plants 9 (3) (2023)
Pradeep Kumar Prabhakar, Jose Henrique Pereira, Rahil Taujale, Wanchen Shao, Vivek S Bharadwaj, Digantkumar Chapla, Jeong-Yeh Yang, Yannick J Bomble, Kelley W Moremen, Natarajan Kannan, Michal Hammel, Paul D Adams, Henrik Vibe Scheller, Breeanna R Urbanowicz
Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature plants (2023)
Thomas C Terwilliger, Pavel V Afonine, Dorothee Liebschner, Tristan I Croll, Airlie J McCoy, Robert D Oeffner, Christopher J Williams, Billy K Poon, Jane S Richardson, Randy J Read, Paul D Adams
Accelerating crystal structure determination with iterative AlphaFold prediction. Acta crystallographica. Section D, Structural biology 79 (Pt 3) (2023)
Dorothee Liebschner, Nigel W Moriarty, Billy K Poon, Paul D Adams
In situ ligand restraints from quantum-mechanical methods. Acta crystallographica. Section D, Structural biology 79 (Pt 2) (2023)
Thomas C Terwilliger, Pavel V Afonine, Dorothee Liebschner, Tristan I Croll, Airlie J McCoy, Robert D Oeffner, Christopher J Williams, Billy K Poon, Jane S Richardson, Randy J Read, Paul D Adams
Accelerating crystal structure determination with iterative AlphaFold prediction. Acta crystallographica. Section D, Structural biology 79 (Pt 3) (2023)
Pradeep Kumar Prabhakar, Jose Henrique Pereira, Rahil Taujale, Wanchen Shao, Vivek S Bharadwaj, Digantkumar Chapla, Jeong-Yeh Yang, Yannick J Bomble, Kelley W Moremen, Natarajan Kannan, Michal Hammel, Paul D Adams, Henrik Vibe Scheller, Breeanna R Urbanowicz
Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature plants (2023)
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J Kaminsky, Miao Zhang, Julia Gätcke, Stephanie Haupt, Isabela I Nangca, Stephen M Keable, A Orkun Aydin, Kensure Tono, Shigeki Owada, Leland B Gee, Franklin D Fuller, Alexander Batyuk, Roberto Alonso Mori, James M Holton, Daniel W Paley, Nigel W Moriarty, Fikret Mamedov, Paul D Adams, Aaron S Brewster, Holger Dobbek, Nicholas K Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan F Kern, Junko Yano, Vittal K Yachandra
Structural evidence for intermediates during O 2 formation in photosystem II. Nature 617 (7961) (2023)
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J Kaminsky, Miao Zhang, Julia Gätcke, Stephanie Haupt, Isabela I Nangca, Stephen M Keable, A Orkun Aydin, Kensure Tono, Shigeki Owada, Leland B Gee, Franklin D Fuller, Alexander Batyuk, Roberto Alonso Mori, James M Holton, Daniel W Paley, Nigel W Moriarty, Fikret Mamedov, Paul D Adams, Aaron S Brewster, Holger Dobbek, Nicholas K Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan F Kern, Junko Yano, Vittal K Yachandra
Structural evidence for intermediates during O 2 formation in photosystem II. Nature (2023)
Jing Dai, Kiera B Wilhelm, Amanda J Bischoff, Jose H Pereira, Michel T Dedeo, Derek M García-Almedina, Paul D Adams, Jay T Groves, Matthew B Francis
A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins. Small (Weinheim an der Bergstrasse, Germany) (2023)
Pavel V Afonine, R W Grosse-Kunstleve, Paul D Adams, A Urzhumtsev
Bulk-solvent and overall scaling revisited: faster calculations, improved results. Corrigendum. Acta crystallographica. Section D, Structural biology (2023)
Jing Huang, Andrew Quest, Pablo Cruz-Morales, Kai Deng, Jose Henrique Pereira, Devon Van Cura, Ramu Kakumanu, Edward E K Baidoo, Qingyun Dan, Yan Chen, Christopher J Petzold, Trent R Northen, Paul D Adams, Douglas S Clark, Emily P Balskus, John F Hartwig, Aindrila Mukhopadhyay, Jay D Keasling
Complete integration of carbene-transfer chemistry into biosynthesis. Nature (2023)
Thomas C Terwilliger, Dorothee Liebschner, Tristan I Croll, Christopher J Williams, Airlie J McCoy, Billy K Poon, Pavel V Afonine, Robert D Oeffner, Jane S Richardson, Randy J Read, Paul D Adams
AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nature methods (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)
Pradeep Kumar Prabhakar, Jose Henrique Pereira, Rahil Taujale, Wanchen Shao, Vivek S Bharadwaj, Digantkumar Chapla, Jeong-Yeh Yang, Yannick J Bomble, Kelley W Moremen, Natarajan Kannan, Michal Hammel, Paul D Adams, Henrik Vibe Scheller, Breeanna R Urbanowicz
Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature plants 9 (3) (2023)
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J Kaminsky, Miao Zhang, Julia Gätcke, Stephanie Haupt, Isabela I Nangca, Stephen M Keable, A Orkun Aydin, Kensure Tono, Shigeki Owada, Leland B Gee, Franklin D Fuller, Alexander Batyuk, Roberto Alonso Mori, James M Holton, Daniel W Paley, Nigel W Moriarty, Fikret Mamedov, Paul D Adams, Aaron S Brewster, Holger Dobbek, Nicholas K Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan F Kern, Junko Yano, Vittal K Yachandra
Structural evidence for intermediates during O 2 formation in photosystem II. Nature 617 (7961) (2023)
Jing Huang, Andrew Quest, Pablo Cruz-Morales, Kai Deng, Jose Henrique Pereira, Devon Van Cura, Ramu Kakumanu, Edward E K Baidoo, Qingyun Dan, Yan Chen, Christopher J Petzold, Trent R Northen, Paul D Adams, Douglas S Clark, Emily P Balskus, John F Hartwig, Aindrila Mukhopadhyay, Jay D Keasling
Complete integration of carbene-transfer chemistry into biosynthesis. Nature 617 (7960) (2023)
Pavel V Afonine, Oleg V Sobolev, Nigel W Moriarty, Thomas C Terwilliger, Paul D Adams
Overall protein structure quality assessment using hydrogen-bonding parameters. Acta crystallographica. Section D, Structural biology (2023)
Asmit Bhowmick, Rana Hussein, Isabel Bogacz, Philipp S Simon, Mohamed Ibrahim, Ruchira Chatterjee, Margaret D Doyle, Mun Hon Cheah, Thomas Fransson, Petko Chernev, In-Sik Kim, Hiroki Makita, Medhanjali Dasgupta, Corey J Kaminsky, Miao Zhang, Julia Gätcke, Stephanie Haupt, Isabela I Nangca, Stephen M Keable, A Orkun Aydin, Kensure Tono, Shigeki Owada, Leland B Gee, Franklin D Fuller, Alexander Batyuk, Roberto Alonso Mori, James M Holton, Daniel W Paley, Nigel W Moriarty, Fikret Mamedov, Paul D Adams, Aaron S Brewster, Holger Dobbek, Nicholas K Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan F Kern, Junko Yano, Vittal K Yachandra
Structural evidence for intermediates during O 2 formation in photosystem II. Nature 617 (7961) (2023)
Jing Huang, Andrew Quest, Pablo Cruz-Morales, Kai Deng, Jose Henrique Pereira, Devon Van Cura, Ramu Kakumanu, Edward E K Baidoo, Qingyun Dan, Yan Chen, Christopher J Petzold, Trent R Northen, Paul D Adams, Douglas S Clark, Emily P Balskus, John F Hartwig, Aindrila Mukhopadhyay, Jay D Keasling
Complete integration of carbene-transfer chemistry into biosynthesis. Nature 617 (7960) (2023)
Thomas C Terwilliger, Pavel V Afonine, Dorothee Liebschner, Tristan I Croll, Airlie J McCoy, Robert D Oeffner, Christopher J Williams, Billy K Poon, Jane S Richardson, Randy J Read, Paul D Adams
Accelerating crystal structure determination with iterative AlphaFold prediction. Acta crystallographica. Section D, Structural biology 79 (Pt 3) (2023)
Dorothee Liebschner, Nigel W Moriarty, Billy K Poon, Paul D Adams
In situ ligand restraints from quantum-mechanical methods. Acta crystallographica. Section D, Structural biology 79 (Pt 2) (2023)
Pavel V Afonine, Paul D Adams, Alexandre G Urzhumtsev
Efficient structure-factor modeling for crystals with multiple components. Acta crystallographica. Section A, Foundations and advances (2023)
Albert K Liu, Jose H Pereira, Alexander J Kehl, Daniel J Rosenberg, Douglas J Orr, Simon K S Chu, Douglas M Banda, Michal Hammel, Paul D Adams, Justin B Siegel, Patrick M Shih
Structural plasticity enables evolution and innovation of RuBisCO assemblies. Science advances 8 (34) (2022)
Thomas C Terwilliger, Billy K Poon, Pavel V Afonine, Christopher J Schlicksup, Tristan I Croll, Claudia Millán, Jane S Richardson, Randy J Read, Paul D Adams
Improved AlphaFold modeling with implicit experimental information. Nature methods 19 (11) (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)
Thomas C Terwilliger, Oleg V Sobolev, Pavel V Afonine, Paul D Adams, Chi Min Ho, Xiaorun Li, Z Hong Zhou
Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. Acta crystallographica. Section D, Structural biology 77 (Pt 4) (2021)
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Nick V Grishin, Lisa N Kinch, R Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R Glassman, Andy DeGiovanni, Jose H Pereira, Andria V Rodrigues, Alberdina A van Dijk, Ana C Ebrecht, Diederik Johannes Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K Christopher Garcia, Nick V Grishin, Paul D Adams, Randy J Read, Julien S Baker
Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.) 373 (6557) (2021)
Catherine L Lawson, Andriy Kryshtafovych, Paul D Adams, Pavel V Afonine, Matthew L Baker, Benjamin A Barad, Paul S Bond, Tom Burnley, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kevin D Cowtan, Ken A Dill, Frank DiMaio, Daniel P Farrell, James S Fraser, Mark A Herzik, Soon Wen Hoh, Jie Hou, Li-Wei Hung, Maxim Igaev, Agnel-Praveen Joseph, Daisuke Kihara, Dilip Kumar, Sumit Mittal, Bohdan Monastyrskyy, Mateusz Olek, Colin M Palmer, Ardan Patwardhan, Alberto Perez, Jonas Pfab, Grigore D Pintilie, Jane S Richardson, Peter B Rosenthal, Daipayan Sarkar, Luisa U Schäfer, Michael F Schmid, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Genki Terashi, Thomas C Terwilliger, Andrea C Vaiana, Liguo Wang, Zhe Wang, Stephanie A Wankowicz, Christopher J Williams, Martyn D Winn, Tianqi Wu, Xiaodi Yu, Kaiming Zhang, Helen M Berman, Wah Chiu
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature methods 18 (2) (2021)
Rana Hussein, Mohamed Ibrahim, Asmit Bhowmick, Philipp S Simon, Ruchira Chatterjee, Louise Lassalle, Margaret Doyle, Isabel Bogacz, In-Sik Kim, Mun Hon Cheah, Sheraz Gul, Casper de Lichtenberg, Petko Chernev, Cindy C Pham, Iris D Young, Sergio Carbajo, Franklin D Fuller, Roberto Alonso Mori, Alex Batyuk, Kyle D Sutherlin, Aaron S Brewster, Robert Bolotovsky, Derek Mendez, James M Holton, Nigel W Moriarty, Paul D Adams, Uwe Bergmann, Nicholas K Sauter, Holger Dobbek, Johannes Messinger, Athina Zouni, Jan F Kern, Vittal K Yachandra, Junko Yano
Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition. Nature communications 12 (1) (2021)
Dorothee Liebschner, Pavel V Afonine, Nigel W Moriarty, Billy K Poon, Vincent B Chen, Paul D Adams
CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta crystallographica. Section D, Structural biology 77 (Pt 1) (2021)
Thomas C Terwilliger, Oleg V Sobolev, Pavel V Afonine, Paul D Adams, Randy J Read
Density modification of cryo-EM maps. Acta crystallographica. Section D, Structural biology 76 (Pt 10) (2020)
Nigel W Moriarty, Pawel A Janowski, Jason M Swails, Hai Nguyen, Jane S Richardson, David A Case, Paul D Adams
Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta crystallographica. Section D, Structural biology 76 (Pt 1) (2020)
Nigel W Moriarty, Dorothee Liebschner, Dale E Tronrud, Paul D Adams
Arginine off-kilter: guanidinium is not as planar as restraints denote. Acta crystallographica. Section D, Structural biology 76 (Pt 12) (2020)
Nigel W Moriarty, Paul D Adams
Iron-sulfur clusters have no right angles. Acta crystallographica. Section D, Structural biology 75 (Pt 1) (2019)
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley J Hintze, Li-Wei Hung, Swati Jain, Airlie J McCoy, Nigel W Moriarty, Robert D Oeffner, Billy K Poon, Michael G Prisant, Randy J Read, Jane S Richardson, David C Richardson, Massimo D Sammito, Oleg V Sobolev, Duncan H Stockwell, Thomas C Terwilliger, Alexandre G Urzhumtsev, Lizbeth L Videau, Christopher J Williams, Paul D Adams
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta crystallographica. Section D, Structural biology 75 (Pt 10) (2019)
Paul D Adams, Pavel V Afonine, Kumaran Baskaran, Helen M Berman, John Berrisford, Gerard Bricogne, David G Brown, Stephen K Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas, Jeffrey C Hoch, Yasuyo Ikegawa, Yumiko Kengaku, Eugene Krissinel, Genji Kurisu, Yu-He Liang, Dorothee Liebschner, Lora Mak, John L Markley, Nigel W Moriarty, Garib N Murshudov, Martin Noble, Ezra Peisach, Irina Persikova, Billy K Poon, Oleg V Sobolev, Eldon L Ulrich, Sameer Velankar, Clemens Vonrhein, John D Westbrook, Marcin Wojdyr, Masashi Yokochi, Jasmine Y Young
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta crystallographica. Section D, Structural biology 75 (Pt 4) (2019)
Pavel V Afonine, Bruno P Klaholz, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams, Alexandre Urzhumtsev
New tools for the analysis and validation of cryo-EM maps and atomic models. Acta crystallographica. Section D, Structural biology 74 (Pt 9) (2018)

Paul D Adams.css-eqlu8i{font-size:small;padding-left:4px;} (P D Adams, Paul Adams)

Publication Activity (10 Years)

Top Topics

Top Venues

Paul D Adams (P D Adams, Paul Adams)