Adams, Paul D.

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

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

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

MolProbity: More and better reference data for improved all‐atom structure validation

Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., et al. (2018) · Protein Science

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 4,599

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

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

Barad, B. A., Echols, N., Wang, R. Y.-R., Cheng, Y., DiMaio, F., Adams, P. D., & Fraser, J. S. (2015) · Nature Methods

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 886

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

Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli

Liu, C.-L., Tian, T., Alonso-Gutierrez, J., Garabedian, B., Wang, S., Baidoo, E. E. K., Benites, V., Chen, Y., Petzold, C. J., Adams, P. D., et al. (2018) · Biotechnology for Biofuels

Microbial Metabolic Engineering and BioproductionPlant biochemistry and biosynthesis

Cited by 70

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

A putative rhamnogalacturonan-II CMP-β-Kdo transferase identified using CRISPR/Cas9 gene edited callus to circumvent embryo lethality

Zhang, Y., Sharma, D., Liang, Y., Downs, N., Dolman, F., Thorne, K., Black, I. M., Pereira, J. H., Adams, P., Scheller, H. V., et al. (2023) · PLANT PHYSIOLOGY

Polysaccharides and Plant Cell WallsPlant Reproductive Biology

Cited by 17

Biosensor-Driven Strain Engineering Reveals Key Cellular Processes for Maximizing Isoprenol Production in Pseudomonas putida

Menasalvas, J., Kulakowski, S., Chen, Y., Gin, J. W., Turumtay, E. A., Baral, N. R., Apolonio, M. A., Rivier, A., Yunus, I. S., Garber, M. E., et al. (2025) · Science Advances

Microbial Metabolic Engineering and BioproductionPlant biochemistry and biosynthesis

Cited by 10

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