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Python-based Hierarchical ENvironment for Integrated Xtallography
 

PHENIX data downloads

Contact: Tom Terwilliger, [email protected]

Accelerating crystal structure determination with iterative AlphaFold prediction Thomas C. Terwilliger, Pavel V. Afonine, Dorothee Liebschner, Tristan I. Croll, Airlie J. McCoy, Robert D. Oeffner, Christopher J. Williams, Billy K. Poon, Jane. S. Richardson, Randy J. Read and Paul D. Adams. Acta Cryst. (2023). D79, 234-244.
Thomas C. Terwilliger, Pavel V. Afonine, Dorothee Liebschner, Tristan I. Croll, Airlie J. McCoy, Robert D. Oeffner, Christopher J. Williams, Billy K. Poon, Jane. S. Richardson, Randy J. Read and Paul D. Adams. AlphaFold predictions are valuable hypotheses, and accelerate but do not replace experimental structure determination. Nature Methods, in press and bioRxiv 2022.11.21.517405
You can find predicted models, rebuilt models, and map coefficients for all datasets at: alphafold_crystallography_2022

Improved AlphaFold modeling with implicit experimental information Thomas C. Terwilliger, Billy K. Poon, Pavel V. Afonine, Christopher J. Schlicksup, Tristan I. Croll, Claudia Millan, Jane S. Richardson, Randy J. Read and Paul D. Adams (2022). Nature Methods 19, 1376-1382.
You can find maps and models at: alphafold_with_density_2022

Improvement of cryo-EM maps by density modification Thomas C. Terwilliger, Steven J. Ludtke, Randy J. Read, Paul D. Adams, Pavel V. Afonine
You can find maps and data used to generate figures at: denmod_2020

A fully automatic method yielding initial models from high-resolution electron cryo-microscopy maps Thomas C. Terwilliger, Paul D. Adams, Pavel V. Afonine, Oleg V. Sobolev
You can find the spreadsheets used in the analyses in this paper and all the automatically-built models and parameters used to generate them at: map_to_model_2018

Macromolecular X-ray structure determination using weak anomalous data Gábor Bunkóczi, Airlie J. McCoy, Nathaniel Echols, Ralf W. Grosse-Kunstleve, Paul D. Adams, Randy J. Read, Thomas C. Terwilliger
You can find the spreadsheets used in the analyses in this paper and the scaled, merged data used in Fig. 2 at: sad_2014

Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization Frank DiMaio, Thomas C. Terwilliger, Randy J. Read, Alexander Wlodawer, Gustav Oberdorfer, Eugene Valkov, Assaf Alon, Deborah Fass, Herbert L. Axelrod, Debanu Das, Sergey M. Vorobiev, Hideo Iwai, P. Raj Pokkuluri & David Baker
You can find the raw data used in the analyses in this paper at: rosetta_2011

Ligand identification using electron-density map correlations. T. C. Terwilliger, P. D. Adams, N. W. Moriarty and J. D. Cohn Acta Cryst. D63, 101-107 (2007)
 [pdf]
You can find the unique ligand set used in the analyses in this paper at: ligand_2006

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty P. H. Zwart, R. J. Read, D. Turk and L.-W. Hung Acta Cryst. D63, 597-610 (2007)
 [pdf]
You can find the models used in the analyses in this paper at: mult_models_2006

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. T. C. Terwilliger, P. D. Adams, R. J. Read, A. J. McCoy, N. W. Moriarty, R. W. Grosse-Kunstleve, P. V. Afonine, P. H. Zwart and L.-W. Hung Acta Cryst. D65, 582-601 (2009)
 		[pdf]
You can find the data and spreadsheets in the analyses in this paper at: scoring_2009