🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Pavel V. Afonine

Lawrence Berkeley National Laboratory

ORCID: 0000-0002-5052-991X
Materials ScienceBiochemistry, Genetics and Molecular BiologyComputer 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 3%percentile
1.2Author DataRank

Indexed papers

2in 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 2 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 →

Top data-sharing exemplar

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

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Nature Methods(2024)10.1038/s41592-024-02321-7
Top 23%
0.871DataRank
Top 23%18 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent B. Chen +76 more

Papers

Driven by 29 papers — median percentile 64. Top paper: “PHENIX: a comprehensive Python-based system for macromolecular structure solution”.

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

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Nature Methods(2024)10.1038/s41592-024-02321-7
Top 23%
0.871DataRank
Top 23%18 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent B. Chen +76 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

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

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

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

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

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

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
0DataRank · unranked
13 citations

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

Detection of translational noncrystallographic symmetry in Patterson functions

Acta Crystallographica Section D Structural Biology(2021)10.1107/s2059798320016836
N/A
0DataRank · unranked
10 citations

Massimo Sammito, Pavel V. Afonine, Isabel Usón, Randy J. Read, Airlie J. McCoy +1 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

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
0DataRank · unranked
49 citations

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

Conformational space exploration of cryo-EM structures by variability refinement

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.23.521827
N/A
0DataRank · unranked
4 citations

Alexia Gobet, Loïck Moissonnier, Billy K. Poon, Vincent Chaptal, Pavel V. Afonine

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
0DataRank · unranked
359 citations

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

Conformational space exploration of cryo-EM structures by variability refinement

Biochimica et Biophysica Acta (BBA) - Biomembranes(2023)10.1016/j.bbamem.2023.184133
N/A
0DataRank · unranked
19 citations

Alexia Gobet, Loïck Moissonnier, Juliette Martin, Billy K. Poon, Vincent Chaptal +1 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

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

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

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

Research Square(2024)10.21203/rs.3.rs-3864137/v1
N/A
0DataRank · unranked
2 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent Chen +76 more

AQuaRef: machine learning accelerated quantum refinement of protein structures

Nature Communications(2025)10.1038/s41467-025-64313-1
N/A
0DataRank · unranked
11 citations

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

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