Pavel V Afonine (Pavel Afonine, P V Afonine)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 29

Top Topics

Density Functional Theory

Positive Airway Pressure

Machine Learning

Electron Microscopy

Top Venues

Acta crystallographica. Section D, Structural biology

Acta crystallographica. Section A, Foundations and advances

Protein science : a publication of the Protein Society

bioRxiv : the preprint server for biology

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

Publications

Alexandre G Urzhumtsev, Paul D Adams, Pavel V Afonine
Universal parameters of bulk-solvent masks. Acta crystallographica. Section A, Foundations and advances 80 (Pt 2) (2024)
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
AQuaRef: Machine learning accelerated quantum refinement of protein structures. bioRxiv : the preprint server for biology (2024)
Pavel V Afonine, Paul D Adams, Oleg V Sobolev, Alexandre G Urzhumtsev
Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein science : a publication of the Protein Society 33 (3) (2024)
Pavel V Afonine, Paul D Adams, Oleg V Sobolev, Alexandre G Urzhumtsev
Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein science : a publication of the Protein Society 33 (3) (2024)
Pavel V Afonine, Paul D Adams, Oleg V Sobolev, Alexandre G Urzhumtsev
Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein science : a publication of the Protein Society 33 (3) (2024)
Alexandre G Urzhumtsev, Paul D Adams, Pavel V Afonine
Universal parameters of bulk-solvent masks. Acta crystallographica. Section A, Foundations and advances (2024)
Alexandre G Urzhumtsev, Paul D Adams, Pavel V Afonine
Universal parameters of bulk-solvent masks. Acta crystallographica. Section A, Foundations and advances 80 (Pt 2) (2024)
Pavel V Afonine, Paul D Adams, Oleg V Sobolev, Alexandre G Urzhumtsev
Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein science : a publication of the Protein Society 33 (3) (2024)
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
AQuaRef: Machine learning accelerated quantum refinement of protein structures. bioRxiv : the preprint server for biology (2024)
Alexandre G Urzhumtsev, Paul D Adams, Pavel V Afonine
Universal parameters of bulk-solvent masks. Acta crystallographica. Section A, Foundations and advances 80 (Pt 2) (2024)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Lum Wang, Holger Kruse, Oleg V Sobolev, Nigel W Moriarty, Mark P Waller, Pavel V Afonine, Malgorzata Biczysko
Real-space quantum-based refinement for cryo-EM: Q|R#3. Acta crystallographica. Section D, Structural biology 76 (Pt 12) (2020)
Min Zheng, Malgorzata Biczysko, Yanting Xu, Nigel W Moriarty, Holger Kruse, Alexandre Urzhumtsev, Mark P Waller, Pavel V Afonine
Including crystallographic symmetry in quantum-based refinement: Q|R#2. Acta crystallographica. Section D, Structural biology 76 (Pt 1) (2020)
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)
Dorothee Liebschner, Pavel V Afonine, Nigel W Moriarty, Paul Langan, Paul D Adams
Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta crystallographica. Section D, Structural biology 74 (Pt 8) (2018)
Thomas C Terwilliger, Oleg V Sobolev, Pavel V Afonine, Paul D Adams
Automated map sharpening by maximization of detail and connectivity. Acta crystallographica. Section D, Structural biology 74 (Pt 6) (2018)
Pavel V Afonine, Paul D Adams, Alexandre Urzhumtsev
From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. Acta crystallographica. Section D, Structural biology 74 (Pt 7) (2018)
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)
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams
Real-space refinement in PHENIX for cryo-EM and crystallography. Acta crystallographica. Section D, Structural biology 74 (Pt 6) (2018)