Author

R. J. Read

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· 6 Biophysics· 5

Signature Assays, Organisms & Methods

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Approach:deep learning· 7 Research Focus:protein structure prediction· 7 Assay:cryo-EM· 4 Assay:protein structure· 4 Approach:statistical model· 4 Research Focus:benchmarking· 2 Approach:experimental assay· 2 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

T. C. Terwilliger· 7 shared A. J. McCoy· 6 shared P. D. Adams· 4 shared B. K. Poon· 3 shared J. S. Richardson· 3 shared P. Afonine· 3 shared T. I. Croll· 3 shared C. J. Williams· 2 shared

Activity by Year

2019-2022 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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7 shared papersBiochemistry

T. C. Terwilliger

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Author profile →

11 papers

Recent·Most cited

Likelihood-based docking of models into cryo-EM maps

C. Millan, A. J. McCoy, T. C. Terwilliger, R. J. Read

This paper introduces a likelihood-based method for docking models into cryo-EM maps, improving speed and accuracy by using expected log-likelihood-gain scores.

bioRxiv · Dec 20, 2022Biophysics

Likelihood-based signal and noise analysis for docking of models into cryo-EM maps

R. J. Read, C. Millan, A. J. McCoy, T. C. Terwilliger

The paper develops a likelihood-based method to analyze signal and noise in cryo-EM maps for improved model docking.

bioRxiv · Dec 20, 2022Biophysics

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

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

The paper evaluates high-confidence AlphaFold predictions against experimental crystal structures, showing they are accurate but require experimental validation for detailed structural features.

bioRxiv · Nov 21, 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

Improved AlphaFold modeling with implicit experimental information

T. C. Terwilliger, B. K. Poon, P. Afonine, C. J. Schlicksup, T. I. Croll, C. Millan-Nebot, J. S. Richardson, R. J. Read, P. D. Adams

The paper improves AlphaFold modeling by incorporating experimental density maps iteratively, resulting in more accurate protein structure predictions.

bioRxiv · Jan 7, 2022Biochemistry

Possible Implications of AlphaFold2 for Crystallographic Phasing by Molecular Replacement

A. J. McCoy, M. D. Sammito, R. J. Read

The paper explores how AlphaFold2's accurate protein structure models may impact crystallographic phasing methods, particularly molecular replacement.

bioRxiv · May 18, 2021Biophysics

Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data

K. S. Hatti, A. J. McCoy, R. J. Read

The paper introduces a likelihood-based method to estimate substructure content from SAD intensity data, accounting for measurement errors and correlations between Bijvoet mates.

bioRxiv · Feb 7, 2021Biophysics

Adaptive conformational restraints for interactive model rebuilding in Cartesian and torsion space

T. I. Croll, R. J. Read

The paper introduces two new adaptive restraint potentials for model rebuilding in molecular modeling, demonstrating their implementation in ISOLDE and applications in real-world examples.

bioRxiv · Sep 29, 2020Biophysics

Density modification of cryo-EM maps

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

The paper examines density modification for cryo-EM maps and presents a procedure to incorporate model-based information while reducing model bias.

bioRxiv · May 13, 2020Biochemistry

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

An oligomeric state-dependent switch in FICD regulates AMPylation and deAMPylation of the chaperone BiP

L. A. Perera, C. Rato, Y. Yan, L. Neidhardt, S. H. McLaughlin, R. J. Read, S. Preissler, D. Ron

This paper identifies how FICD switches between AMPylation and deAMPylation of BiP by changing its oligomeric state, regulated by ATP/ADP levels.

bioRxiv · Apr 1, 2019Biochemistry