Author

P. V. Afonine

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 5 Biophysics· 1

Signature Assays, Organisms & Methods

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Research Focus:protein structure prediction· 6 Assay:cryo-EM· 4 Approach:deep learning· 4 Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:protein structure· 2 Approach:experimental assay· 1 Research Focus:software / tool· 1

Frequent Co-Authors

P. D. Adams· 5 shared T. C. Terwilliger· 4 shared N. W. Moriarty· 2 shared O. V. Sobolev· 2 shared R. J. Read· 2 shared A. J. McCoy· 1 shared A. Perrakis· 1 shared B. K. Poon· 1 shared

Activity by Year

2018-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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5 shared papersBiochemistry

P. D. Adams

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Author profile →

6 papers

Recent·Most cited

Optimal clustering for quantum refinement of biomolecular structures: Q|R#4

Y. Wang, H. Kruse, N. W. Moriarty, M. P. Waller, P. V. Afonine, M. Biczysko

This paper validates and optimizes a divide-and-conquer procedure for quantum refinement of biomolecular structures, introducing an error score to guide computational efficiency.

bioRxiv · Nov 24, 2022Biochemistry

Accelerating crystal structure determination with iterative AlphaFold prediction

T. C. Terwilliger, P. V. Afonine, D. Liebschner, T. I. Croll, A. J. McCoy, R. D. Oeffner, C. J. Williams, B. K. Poon, J. S. Richardson, R. J. Read, P. D. Adams

This paper introduces an iterative AlphaFold method to accelerate crystal structure determination using sequence and crystallographic data, achieving higher accuracy than non-iterative approaches.

bioRxiv · Nov 18, 2022Biochemistry

A global Ramachandran score identifies protein structures with unlikely stereochemistry

O. V. Sobolev, P. V. Afonine, N. W. Moriarty, M. L. Hekkelman, R. P. Joosten, A. Perrakis, P. D. Adams

The paper introduces a re-implemented Ramachandran Z-score and its uncertainty estimation for protein structure validation, advocating its inclusion in structural publications and validation reports.

bioRxiv · Mar 26, 2020Biophysics

Improvement of cryo-EM maps by density modification

T. C. Terwilliger, S. J. Ludtke, R. J. Read, P. D. Adams, P. V. Afonine

This paper introduces a density modification method for improving cryo-EM maps by combining half-map information and a model, enhancing map quality and detail visibility.

bioRxiv · Mar 25, 2020Biochemistry

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

T. C. Terwilliger, P. D. Adams, P. V. Afonine, O. V. Sobolev

The paper develops a fully automatic method for optimizing and interpreting cryo-EM maps, achieving 71% residue reproduction for high-resolution reconstructions.

bioRxiv · Feb 16, 2018Biochemistry

Automated map sharpening by maximization of detail and connectivity

T. C. Terwilliger, O. Sobolev, P. V. Afonine, P. D. Adams

The paper develops an algorithm to automatically sharpen cryo-EM maps by optimizing detail and connectivity, showing it improves map quality compared to model-based methods.

bioRxiv · Jan 11, 2018Biochemistry