Paul D. Adams

Also affiliated with University of California, Berkeley

Biochemistry, Genetics and Molecular BiologyPhysics and AstronomyEnvironmental Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 2%percentile

2.9Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167599

Top 10%

2.1DataRank

Top 10%95 citations

Jasmine Young, Chenghua Shao, Zukang Feng, Vladimir Guranović, Catherine L. Lawson +17 more

Papers

Driven by 61 papers — median percentile 52. Top paper: “Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism”.

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2000529117

N/A

4.8DataRank · unranked

239 citations

Thomas Fransson, Ruchira Chatterjee, Mun Hon Cheah, Rana Hussein, Louise Lassalle +34 more

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167599

Top 10%

2.1DataRank

Top 10%95 citations

Jasmine Young, Chenghua Shao, Zukang Feng, Vladimir Guranović, Catherine L. Lawson +17 more

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Acta Crystallographica Section D Biological Crystallography(2010)10.1107/s0907444909052925

N/A

1.5DataRank · unranked

24351 citations

Pavel V. Afonine, Gábor Bunkóczi, Vincent B. Chen, Ian W. Davis, Nathaniel Echols +19 more

Phasercrystallographic software

Journal of Applied Crystallography(2007)10.1107/s0021889807021206

N/A

1.5DataRank · unranked

20761 citations

Ralf W. Grosse-Kunstleve, Paul D. Adams, Martyn D. Winn, Laurent C. Storoni, Randy J. Read +3 more

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

Acta Crystallographica Section D Biological Crystallography(1998)10.1107/s0907444998003254

N/A

1.4DataRank · unranked

15776 citations

G. M. Clore, W. L. DeLano, Ralf W. Grosse-Kunstleve, J. S. Jiang, J. Kuszewski +20 more

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination

Nature Methods(2023)10.1038/s41592-023-02087-4

N/A

0.884DataRank · unranked

362 citations

Dorothée Liebschner, Tristan I. Croll, Christopher J. Williams, Airlie J. McCoy, Billy K. Poon +6 more

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

Nature Communications(2023)10.1038/s41467-023-37254-w

N/A

0.686DataRank · unranked

96 citations

Suman Pokhrel, Audrey Labbé, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson +28 more

Complete integration of carbene-transfer chemistry into biosynthesis

Nature(2023)10.1038/s41586-023-06027-2

N/A

0.635DataRank · unranked

68 citations

Andrew F. G. Quest, Pablo Cruz‐Morales, Kai Deng, J.H. Pereira, Devon Van Cura +13 more

AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.21.517405

N/A

0.587DataRank · unranked

49 citations

Dorothée Liebschner, Tristan I. Croll, Christopher J. Williams, Airlie J. McCoy, Billy K. Poon +6 more

Community recommendations on cryoEM data archiving and validation

IUCrJ(2024)10.1107/s2052252524001246

N/A

0.542DataRank · unranked

36 citations

Paul D. Adams, Sarah J. Butcher, Catherine L. Lawson, Alexis Rohou, Peter B. Rosenthal +42 more

Structural and biochemical insight into a modular β-1,4-galactan synthase in plants

Nature Plants(2023)10.1038/s41477-023-01358-4

N/A

0.396DataRank · unranked

13 citations

J.H. Pereira, Rahil Taujale, Wanchen Shao, Vivek S. Bharadwaj, Digantkumar Chapla +9 more

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

Acta Crystallographica Section D Structural Biology(2021)10.1107/s2059798321001765

N/A

0.396DataRank · unranked

13 citations

Oleg V. Sobolev, Pavel V. Afonine, Paul D. Adams, Chi-Min Ho, Xiaorun Li +2 more

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

Acta Crystallographica Section D Structural Biology(2024)10.1107/s2059798324006776

N/A

0.394DataRank · unranked

8 citations

Eric F. Pettersen, Airlie J. McCoy, Tristan I. Croll, Thomas C. Terwilliger, Billy K. Poon +4 more

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.147033

Top 48%

0.375DataRank

Top 48%7 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

AQuaRef: machine learning accelerated quantum refinement of protein structures

Nature Communications(2025)10.1038/s41467-025-64313-1

N/A

0.373DataRank · unranked

11 citations

Małgorzata Biczysko, Kavindri Ranasinghe, Nigel W. Moriarty, Hatice Gökcan, Holger Kruse +7 more

The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity

Journal of Biological Chemistry(2024)10.1016/j.jbc.2024.107921

N/A

0.365DataRank · unranked

5 citations

J.H. Pereira, Andy DeGiovanni, R.P. McAndrew, Malathy Palayam, Jedidiah O. Peek +6 more

ALS-ENABLE: creating synergy and opportunity at the Advanced Light Source synchrotron structural biology beamlines

Journal of Synchrotron Radiation(2025)10.1107/s1600577525004205

Top 50%

0.349DataRank

Top 50%7 citations

Sayan Gupta, Joshua T. Del Mundo, Aimee Chi Soe, Brandon K. Russell, Behzad Rad +22 more

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Journal of Biological Chemistry(2024)10.1016/j.jbc.2024.107736

N/A

0.300DataRank · unranked

5 citations

Nigel W. Moriarty, Ramu Kakumanu, Andy DeGiovanni, J.H. Pereira, Jennifer Gin +5 more

Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map

Proceedings of the National Academy of Sciences(2021)10.1073/pnas.2102342118

N/A

0DataRank · unranked

16 citations

Nigel W. Moriarty, Jan Kern, James M. Holton, Aaron S. Brewster, Asmit Bhowmick +9 more

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

Research Square(2021)10.21203/rs.3.rs-906621/v1

N/A

0DataRank · unranked

13 citations

Suman Pohkrel, Audrey Labbé, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson +21 more

Improved AlphaFold modeling with implicit experimental information

Nature Methods(2022)10.1038/s41592-022-01645-6

N/A

0DataRank · unranked

138 citations

Billy K. Poon, Pavel V. Afonine, Christopher J. Schlicksup, Tristan I. Croll, Claudia Millán +4 more

Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease

Scientific Reports(2022)10.1038/s41598-022-15930-z

N/A

0DataRank · unranked

47 citations

D. Kumaran, Dale F. Kreitler, Alexei S. Soares, Jantana Keereetaweep, Jean Jakoncic +10 more

Integration of software tools for integrative modeling of biomolecular systems

Journal of Structural Biology(2022)10.1016/j.jsb.2022.107841

N/A

0DataRank · unranked

19 citations

Thomas-Otavio Peulen, Benjamin Webb, Billy K. Poon, James S. Fraser, Paul D. Adams +2 more

Improved AlphaFold modeling with implicit experimental information

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.07.475350

N/A

0DataRank · unranked

28 citations

Billy K. Poon, Pavel V. Afonine, Christopher J. Schlicksup, Tristan I. Croll, Claudia Millán +4 more

Accelerating crystal structure determination with iterative AlphaFold prediction

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.11.18.517112

N/A

0DataRank · unranked

7 citations

Pavel V. Afonine, Dorothée Liebschner, Tristan I. Croll, Airlie J. McCoy, Robert D. Oeffner +6 more

A membrane-associated light harvesting model is enabled by functionalized assemblies of gene-doubled TMV proteins

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.08.507180

N/A

0DataRank · unranked

0 citations

Kiera B. Wilhelm, Amanda J. Bischoff, J.H. Pereira, Michel T. Dedeo, Derek García-Almedina +4 more

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

Research Square(2022)10.21203/rs.3.rs-906621/v2

N/A

0DataRank · unranked

0 citations

Suman Pokhrel, Audrey Labbé, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson +28 more

Structural evidence for intermediates during O2 formation in photosystem II

Nature(2023)10.1038/s41586-023-06038-z

N/A

0DataRank · unranked

171 citations

Rana Hussein, Isabel Bogacz, Philipp S. Simon, Mohamed Ibrahim, Ruchira Chatterjee +35 more

Accelerating crystal structure determination with iterative AlphaFold prediction

Acta Crystallographica Section D Structural Biology(2023)10.1107/s205979832300102x

N/A

0DataRank · unranked

58 citations

Pavel V. Afonine, Dorothée Liebschner, Tristan I. Croll, Airlie J. McCoy, Robert D. Oeffner +6 more

Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics

Nature Catalysis(2023)10.1038/s41929-022-00899-9

N/A

0DataRank · unranked

24 citations

Sean N. Natoli, Marc Garcia‐Borràs, J.H. Pereira, Derek B. Hu, Paul D. Adams +4 more

In situ ligand restraints from quantum-mechanical methods

Acta Crystallographica Section D Structural Biology(2023)10.1107/s2059798323000025

N/A

0DataRank · unranked

21 citations

Nigel W. Moriarty, Billy K. Poon, Paul D. Adams, Dorothée Liebschner

A Membrane‐Associated Light‐Harvesting Model is Enabled by Functionalized Assemblies of Gene‐Doubled TMV Proteins

Small(2023)10.1002/smll.202207805

N/A

0DataRank · unranked

11 citations

Kiera B. Wilhelm, Amanda J. Bischoff, J.H. Pereira, Michel T. Dedeo, Derek García-Almedina +4 more

Improved joint X-ray and neutron refinement procedure in Phenix

Acta Crystallographica Section D Structural Biology(2023)10.1107/s2059798323008914

N/A

0DataRank · unranked

11 citations

Pavel V. Afonine, Billy K. Poon, Nigel W. Moriarty, Paul D. Adams, Dorothée Liebschner

A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening

Lab on a Chip(2023)10.1039/d2lc00980c

N/A

0DataRank · unranked

10 citations

Jenny R. Onley, Kai Deng, Peter Andeer, Benjamin P. Bowen, Kshitiz Gupta +10 more

Overall protein structure quality assessment using hydrogen-bonding parameters

Acta Crystallographica Section D Structural Biology(2023)10.1107/s2059798323005077

N/A

0DataRank · unranked

9 citations

Oleg V. Sobolev, Nigel W. Moriarty, Thomas C. Terwilliger, Paul D. Adams, Pavel V. Afonine

Efficient structure-factor modeling for crystals with multiple components

Acta Crystallographica Section A Foundations and Advances(2023)10.1107/s205327332300356x

N/A

0DataRank · unranked

1 citations

Paul D. Adams, Alexandre Urzhumtsev, Pavel V. Afonine

Accounting for nonuniformity of bulk‐solvent: A mosaic model

Protein Science(2024)10.1002/pro.4909

N/A

0DataRank · unranked

9 citations

Paul D. Adams, Oleg V. Sobolev, Alexandre Urzhumtsev, Pavel V. Afonine

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Protein Science(2024)10.1002/pro.4992

N/A

0DataRank · unranked

7 citations

Thomas C. Terwilliger, Paul D. Adams, Billy K. Poon

Universal parameters of bulk-solvent masks

Acta Crystallographica Section A Foundations and Advances(2024)10.1107/s2053273324000299

N/A

0DataRank · unranked

2 citations

Paul D. Adams, Pavel V. Afonine, Alexandre Urzhumtsev

Protonation of histidine rings using quantum-mechanical methods

Acta Crystallographica Section D Structural Biology(2024)10.1107/s2059798324006314

N/A

0DataRank · unranked

2 citations

Jonathan E. Moussa, Paul D. Adams, Nigel W. Moriarty

A cost‐effective enzyme kinetics and inhibition model for biochemistry education and research

Biochemistry and Molecular Biology Education(2024)10.1002/bmb.21845

N/A

0DataRank · unranked

1 citations

Alyssa Teague, Taylor East, Kim Rhona Jacinto, Macie Carter, Jacey Totty +3 more

Enzymology and Structural Basis of Glycosyltransferases Involved in Saponin C28 Carboxylic Acid O - d -Fucosylation

JACS Au(2025)10.1021/jacsau.5c00907

N/A

0DataRank · unranked

1 citations

J.H. Pereira, Peter H. Winegar, David M. FitzGerald, Andy DeGiovanni, Xiaoyue Chen +11 more

Biochemical and structural characterization of glycosyltransferase family 61 proteins reveal a key determinant of sugar donor specificity

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.18.665579

N/A

0DataRank · unranked

1 citations

J.H. Pereira, Andy DeGiovanni, Pradeep Kumar Prabhakar, Digantkumar Chapla, Kelley W. Moremen +4 more

Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.08.01.668229

N/A

0DataRank · unranked

0 citations

David A. Case, Dorothée Liebschner, Paul D. Adams, Nigel W. Moriarty

A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry

Structure(2020)10.1016/j.str.2020.08.005

N/A

0DataRank · unranked

213 citations

Pavel V. Afonine, Nigel W. Moriarty, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis +2 more

Improvement of cryo-EM maps by density modification

Nature Methods(2020)10.1038/s41592-020-0914-9

N/A

0DataRank · unranked

330 citations

Steven J. Ludtke, Randy J. Read, Paul D. Adams, Pavel V. Afonine, Thomas C. Terwilliger

CERES: a cryo-EM re-refinement system for continuous improvement of deposited models

Acta Crystallographica Section D Structural Biology(2020)10.1107/s2059798320015879

N/A

0DataRank · unranked

22 citations

Pavel V. Afonine, Nigel W. Moriarty, Billy K. Poon, Vincent B. Chen, Paul D. Adams +1 more

Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster

Biochemistry(2020)10.1021/acs.biochem.0c00126

N/A

0DataRank · unranked

15 citations

J.H. Pereira, Marian-Joy Baluyot, Julie Lake, Hendrik Puetz, Daniel J. Rosenburg +3 more

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

Methods in enzymology on CD-ROM/Methods in enzymology(2020)10.1016/bs.mie.2020.01.007

N/A

0DataRank · unranked

17 citations

Pavel V. Afonine, Alexandre Urzhumtsev, Paul D. Adams, Dorothée Liebschner

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

Nature Communications(2020)10.1038/s41467-020-16815-3

N/A

0DataRank · unranked

15 citations

Jacquelyn M. Blake-Hedges, J.H. Pereira, John A. Hangasky, Michael S. Belcher, William M. Moore +16 more

Arginine off-kilter: guanidinium is not as planar as restraints denote

Acta Crystallographica Section D Structural Biology(2020)10.1107/s2059798320013534

N/A

0DataRank · unranked

15 citations

Dorothée Liebschner, Dale E. Tronrud, Paul D. Adams, Nigel W. Moriarty

Density modification of cryo-EM maps

Acta Crystallographica Section D Structural Biology(2020)10.1107/s205979832001061x

N/A

0DataRank · unranked

46 citations

Oleg V. Sobolev, Pavel V. Afonine, Paul D. Adams, Randy J. Read, Thomas C. Terwilliger

What are the current limits on determination of protonation state using neutron macromolecular crystallography?

Methods in enzymology on CD-ROM/Methods in enzymology(2020)10.1016/bs.mie.2020.01.008

N/A

0DataRank · unranked

3 citations

Pavel V. Afonine, Nigel W. Moriarty, Paul D. Adams, Dorothée Liebschner

A global Ramachandran score identifies protein structures with unlikely stereochemistry

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.26.010587

N/A

0DataRank · unranked

16 citations

Pavel V. Afonine, Nigel W. Moriarty, Maarten L. Hekkelman, Robbie P. Joosten, Anastassis Perrakis +2 more

Macromolecular refinement of X-ray and cryo-electron microscopy structures with Phenix / OPLS3e for improved structure and ligand quality

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.07.10.198093

N/A

0DataRank · unranked

6 citations

Nigel W. Moriarty, Oleg V. Sobolev, Paul D. Adams, Kenneth Borrelli, Gydo C. P. van Zundert

Density modification of cryo-EM maps

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.13.091884

N/A

0DataRank · unranked

3 citations

Oleg V. Sobolev, Pavel V. Afonine, Paul D. Adams, Randy J. Read, Thomas C. Terwilliger

Accurate prediction of protein structures and interactions using a three-track neural network

Science(2021)10.1126/science.abj8754

N/A

0DataRank · unranked

5780 citations

Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee +27 more

Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition

Nature Communications(2021)10.1038/s41467-021-26781-z

N/A

0DataRank · unranked

149 citations

Mohamed Ibrahim, Asmit Bhowmick, Philipp S. Simon, Ruchira Chatterjee, Louise Lassalle +29 more

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Nature Methods(2021)10.1038/s41592-020-01051-w

N/A

0DataRank · unranked

119 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality

Structure(2021)10.1016/j.str.2021.03.011

N/A

0DataRank · unranked

69 citations

Nigel W. Moriarty, Oleg V. Sobolev, Paul D. Adams, Kenneth Borrelli, Gydo C. P. van Zundert

Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450

Metabolic Engineering(2021)10.1016/j.ymben.2021.01.004

N/A

0DataRank · unranked

61 citations

J.H. Pereira, Susan E. Tsutakawa, Xinyue Fang, Paul D. Adams, Aindrila Mukhopadhyay +2 more

Paul D. Adams

Indexed papers

Top data-sharing exemplar

Papers