Read, Randy J.

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

Phaser crystallographic software

McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 20,612

Overview of the CCP 4 suite and current developments

Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 12,353

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5,549

PHENIX : building new software for automated crystallographic structure determination

Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography

Enzyme Structure and FunctionCrystal structures of chemical compounds

Cited by 4,361

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

Shiga-like toxins are neutralized by tailored multivalent carbohydrate ligands

Kitov, P. I., Sadowska, J. M., Mulvey, G., Armstrong, G. D., Ling, H., Pannu, N. S., Read, R. J., & Bundle, D. R. (2000) · Nature

Carbohydrate Chemistry and SynthesisEscherichia coli research studies

Cited by 869

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

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

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

Oeffner, R. D., Croll, T. I., Millán, C., Poon, B. K., Schlicksup, C. J., Read, R. J., & Terwilliger, T. C. (2022) · Acta Crystallographica Section D Structural Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 63

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

Assessing the utility of CASP14 models for molecular replacement

Millán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J., & Read, R. J. (2021) · Proteins: Structure, Function, and Bioinformatics

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 62

Likelihood-based docking of models into cryo-EM maps

Millán, C., McCoy, A. J., Terwilliger, T. C., & Read, R. J. (2023) · Acta Crystallographica Section D Structural Biology

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 23

Likelihood-based docking of models into cryo-EM maps

Millán, C., McCoy, A. J., Terwilliger, T. C., & Read, R. J. (2022) · Acta Crystallographica Section D Structural Biology

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 23

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

Fadini, A., Li, M., McCoy, A. J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A. R., Jovine, L., Terwilliger, T. C., et al. (2026) · Nature Methods

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 22

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX

Read, R. J., Pettersen, E. F., McCoy, A. J., Croll, T. I., Terwilliger, T. C., Poon, B. K., Meng, E. C., Liebschner, D., & Adams, P. D. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 1