Pavel V. Afonine - Publications, H-index & Citations

Pavel V. Afonine

lawrence berkeley national laboratory

51H指数

188论文数

6.1W被引数

收录论文 27

发表时间

An additional water is introduced into the manganese cluster during the formation of the S3 state of photosystem II 在光合系统II的S3状态形成过程中，锰簇中引入了一分子水

Nature Communications

IF15.7

2026-08-22

OAAI

Asmit Bhowmick; Miao Zhang; Philipp S. Simon; Hiroki Makita; Isabela I. Nangca; Erzsi Szilagyi; Moritz Kretzschmar; Margaret D. Doyle; Natalie M. Minnetian; Rana Hussein; Olli Hart; Kuntal Chatterjee; A. Orkun Aydin; Dmitry Shevela; Mun Hon Cheah; Nicholas Croy; Petko Chernev; Thomas Fransson; Vandana Tiwari; Humberto Sanchez; Pamela Schleissner; Randy Lemons; Greg Gate; Meredith Henstridge; James M. Glownia; Frédéric Poitevin; Daniel J. Rosenberg; Sebastian Dehe; Leland B. Gee; Kensuke Tono; Shigeki Owada; Roland Oggenfuss; Dmitry Ozerov; Mathias Sander; Roman Mankowsky; Henrik T. Lemke; Iris D. Young; James M. Holton; David W. Mittan-Moreau; Daniel W. Paley; Pavel V. Afonine; Nigel W. Moriarty; Paul D. Adams; Fikret Mamedov; Holger Dobbek; Athina Zouni; Roberto Alonso-Mori; Uwe Bergmann; Aaron S. Brewster; Nicholas K. Sauter; Johannes Messinger; Jan F. Kern; Vittal K. Yachandra; Junko Yano

pyDiSCaMB: enabling the use of multipolar scattering factors in Phenix pyDiSCaMB：在Phenix中启用多极散射因子的使用

Journal of Applied Crystallography

IF2.8

2026-04-01

OAAI

Femoen, Viljar J.; Pacoste, Laura; Chodkiewicz, Michal Leszek; Afonine, Pavel V.; Poon, Billy K.; Kulik, Marta; Golon, Lukasz; Moriarty, Nigel W.; Adams, Paul D.; Hofer, Gerhard; Dominiak, Paulina Maria; Liebschner, Dorothee; Zou, Xiaodong

Author Correction: Macromolecular crystallography 作者更正：Macromolecular crystallography

Nature Reviews Methods Primers

IF56

2025-10-31

OAAI

Pavel V. Afonine; Armando Albert; Kay Diederichs; Juan A. Hermoso; Eugene Krissinel; José Antonio Márquez; Santosh Panjikar; Maria Solà; Andrea Thorn; Isabel Usón

AQuaRef: machine learning accelerated quantum refinement of protein structures AQuaRef：机器学习加速的蛋白质结构量子精修

Nature Communications

IF15.7

2025-10-17

OAAI

Roman Zubatyuk; Malgorzata Biczysko; Kavindri Ranasinghe; Nigel W. Moriarty; Hatice Gokcan; Holger Kruse; Billy K. Poon; Paul D. Adams; Mark P. Waller; Adrian E. Roitberg; Olexandr Isayev; Pavel V. Afonine

Macromolecular crystallography 大分子晶体学

Nature Reviews Methods Primers

IF56

2025-10-09

PREAI

Pavel V. Afonine; Armando Albert; Kay Diederichs; Juan A. Hermoso; Eugene Krissinel; José Antonio Márquez; Santosh Panjikar; Maria Solà; Andrea Thorn; Isabel Usón

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

NATURE METHODS

IF32.1

2024-06-25

OAAI

Lawson, Catherine L.; Kryshtafovych, Andriy; Pintilie, Grigore D.; Burley, Stephen K.; Cerny, Jiri; Chen, Vincent B.; Emsley, Paul; Gobbi, Alberto; Joachimiak, Andrzej; Noreng, Sigrid; Prisant, Michael G.; Read, Randy J.; Richardson, Jane S.; Rohou, Alexis L.; Schneider, Bohdan; Sellers, Benjamin D.; Shao, Chenghua; Sourial, Elizabeth; Williams, Chris I.; Williams, Christopher J.; Yang, Ying; Abbaraju, Venkat; Afonine, Pavel V.; Baker, Matthew L.; Bond, Paul S.; Blundell, Tom L.; Burnley, Tom; Campbell, Arthur; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, K. D.; DiMaio, Frank; Esmaeeli, Reza; Giri, Nabin; Grubmueller, Helmut; Hoh, Soon Wen; Hou, Jie; Hryc, Corey F.; Hunte, Carola; Igaev, Maxim; Joseph, Agnel P.; Kao, Wei-Chun; Kihara, Daisuke; Kumar, Dilip; Lang, Lijun; Lin, Sean; Subramaniya, Sai R. Maddhuri Venkata; Mittal, Sumit; Mondal, Arup; Moriarty, Nigel W.; Muenks, Andrew; Murshudov, Garib N.; Nicholls, Robert A.; Olek, Mateusz; Palmer, Colin M.; Perez, Alberto; Pohjolainen, Emmi; Pothula, Karunakar R.; Rowley, Christopher N.; Sarkar, Daipayan; Schaefer, Luisa U.; Schlicksup, Christopher J.; Schroeder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abhishek; Sobolev, Oleg V.; Terashi, Genki; Vaiana, Andrea C.; Vedithi, Sundeep C.; Verburgt, Jacob; Wang, Xiao; Warshamanage, Rangana; Winn, Martyn D.; Weyand, Simone; Yamashita, Keitaro; Zhao, Minglei; Schmid, Michael F.; Berman, Helen M.; Chiu, Wah

AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination AlphaFold预测是有价值的假设，可以加速但不能替代实验结构确定

NATURE METHODS

IF32.1

2023-11-30

OAAI

Terwilliger, Thomas C.; Liebschner, Dorothee; Croll, Tristan I.; Williams, Christopher J.; McCoy, Airlie J.; Poon, Billy K.; Afonine, Pavel V.; Oeffner, Robert D.; Richardson, Jane S.; Read, Randy J.; Adams, Paul D.

Improved AlphaFold modeling with implicit experimental information 具有隐式实验信息的改进AlphaFold建模

NATURE METHODS

IF32.1

2022-10-20

OAAI

Terwilliger, Thomas C.; Poon, Billy K.; Afonine, Pavel, V; Schlicksup, Christopher J.; Croll, Tristan, I; Millan, Claudia; Richardson, Jane S.; Read, Randy J.; Adams, Paul D.

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

NATURE METHODS

IF32.1

2021-02-04

OAAI

Lawson, Catherine L.; Kryshtafovych, Andriy; Adams, Paul D.; Afonine, Pavel, V; Baker, Matthew L.; Barad, Benjamin A.; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A.; DiMaio, Frank; Farrell, Daniel P.; Fraser, James S.; Herzik, Mark A., Jr.; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P.; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M.; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D.; Richardson, Jane S.; Rosenthal, Peter B.; Sarkar, Daipayan; Schafer, Luisa U.; Schmid, Michael F.; Schroder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C.; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A.; Williams, Christopher J.; Winn, Martyn; Wu, Tianqi; Yu, Xiaodi; Zhang, Kaiming; Berman, Helen M.; Chiu, Wah

Improvement of cryo-EM maps by density modification

NATURE METHODS

IF32.1

2020-08-17

151

OAAI

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

Cryo_fit: Democratization of flexible fitting for cryo-EM

JOURNAL OF STRUCTURAL BIOLOGY

IF5.1

2019-10-01

OAAI

Kim, Doo Nam; Moriarty, Nigel W.; Kirmizialtin, Serdal; Afonine, Pavel, V; Poon, Billy; Sobolev, Oleg, V; Adams, Paul D.; Sanbonmatsu, Karissa

Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge

JOURNAL OF STRUCTURAL BIOLOGY

IF5.1

2018-11-01

OAAI

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

Anomalous X-ray diffraction studies of ion transport in K+ channels

NATURE COMMUNICATIONS

IF15.7

2018-10-31

OAAI

Langan, Patricia S.; Vandavasi, Venu Gopal; Weiss, Kevin L.; Afonine, Pavel V.; el Omari, Kamel; Duman, Ramona; Wagner, Armin; Coates, Leighton

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps

NATURE METHODS

IF32.1

2018-10-30

108

OAAI

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.; Sobolev, Oleg V.

Reply to 'Misreading chaperone-substrate complexes from random noise'

NATURE STRUCTURAL & MOLECULAR BIOLOGY

IF10.1

2018-10-08

PREAI

Horowitz, Scott; Salmon, Loic; Koldewey, Philipp; Ahlstrom, Logan S.; Martin, Raoul; Quan, Shu; Afonine, Pavel V.; van den Bedem, Henry; Wang, Lili; Xu, Qingping; Trievel, Raymond C.; Brooks, Charles L., III; Bardwell, James C. A.

Accurate model annotation of a near-atomic resolution cryo-EM map 近原子分辨率低温电磁图的精确模型注释

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2017-03-07

101

OAAI

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

NATURE COMMUNICATIONS

IF15.7

2017-01-30

OAAI

Lokareddy, Ravi K.; Sankhala, Rajeshwer S.; Roy, Ankoor; Afonine, Pavel V.; Motwani, Tina; Teschke, Carolyn M.; Parent, Kristin N.; Cingolani, Gino

Visualizing chaperone-assisted protein folding

NATURE STRUCTURAL & MOLECULAR BIOLOGY

IF10.1

2016-05-30

OAAI

An atomic model of brome mosaic virus using direct electron detection and real-space optimization

NATURE COMMUNICATIONS

IF15.7

2014-09-04

106

OAAI

Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J.; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah

Combining Crystallographic and Structure-Modeling Approaches in Macromolecular Crystallography

BIOPHYSICAL JOURNAL

IF3.1

2014-01-01

OAAI

Terwilliger, Thomas C.; DiMaio, Frank; Read, Randy J.; Baker, David; Brunger, Axel T.; Adams, Paul D.; Afonine, Pavel V.; Hung, Li-Wei

研究方向