Afonine, Pavel V.

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

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 23,716

Towards automated crystallographic structure refinement with phenix.refine

Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 5,511

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J., & Adams, P. D. (2008) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 1,462

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

Terwilliger, T. C., Liebschner, D., Croll, T. I., Williams, C. J., McCoy, A. J., Poon, B. K., Afonine, P. V., Oeffner, R. D., Richardson, J. S., Read, R. J., et al. (2022) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 411

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

Terwilliger, T. C., Liebschner, D., Croll, T. I., Williams, C. J., McCoy, A. J., Poon, B. K., Afonine, P. V., Oeffner, R. D., Richardson, J. S., Read, R. J., et al. (2024) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 411

Coupling of receptor conformation and ligand orientation determine graded activity

Bruning, J. B., Parent, A. A., Gil, G., Zhao, M., Nowak, J., Pace, M. C., Smith, C. L., Afonine, P. V., Adams, P. D., Katzenellenbogen, J. A., et al. (2010) · Nature Chemical Biology

Estrogen and related hormone effectsReceptor Mechanisms and Signaling

Cited by 142

Improved AlphaFold modeling with implicit experimental information

Terwilliger, T. C., Poon, B. K., Afonine, P. V., Schlicksup, C. J., Croll, T. I., Millán, C., Richardson, J. S., Read, R. J., & Adams, P. D. (2022) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 140

Improved AlphaFold modeling with implicit experimental information

Terwilliger, T. C., Poon, B. K., Afonine, P. V., Schlicksup, C. J., Croll, T. I., Millán, C., Richardson, J. S., Read, R. J., & Adams, P. D. (2022) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 140

Crystallographic model quality at a glance

Urzhumtseva, L., Afonine, P. V., Adams, P. D., & Urzhumtsev, A. (2009) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 110

Accelerating crystal structure determination with iterative AlphaFold prediction

Terwilliger, T. C., Afonine, P. V., Liebschner, D., Croll, T. I., McCoy, A. J., Oeffner, R. D., Williams, C. J., Poon, B. K., Richardson, J. S., Read, R. J., et al. (2023) · Acta Crystallographica Section D Structural Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 62

Conformational space exploration of cryo-EM structures by variability refinement

Afonine, P. V., Gobet, A., Moissonnier, L., Poon, B. K., & Chaptal, V. (2022) · Biochimica et Biophysica Acta (BBA) - Biomembranes

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 18

Conformational space exploration of cryo-EM structures by variability refinement

Afonine, P. V., Gobet, A., Moissonnier, L., Martin, J., Poon, B. K., & Chaptal, V. (2023) · Biochimica et Biophysica Acta (BBA) - Biomembranes

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 18