All Stories

  1. Universal parameters of bulk-solvent masks

    Article • Acta Crystallographica Section A Foundations and Advances, February 2024, International Union of Crystallography

    Dr Pavel Afonine

  2. Overall protein structure quality assessment using hydrogen-bonding parameters

    Article • Acta Crystallographica Section D Structural Biology, July 2023, International Union of Crystallography

    Dr Pavel Afonine

  3. Efficient structure-factor modeling for crystals with multiple components

    Article • Acta Crystallographica Section A Foundations and Advances, June 2023, International Union of Crystallography

    Dr Pavel Afonine

  4. Bulk-solvent and overall scaling revisited: faster calculations, improved results. Corrigendum.

    Article • Acta Crystallographica Section D Structural Biology, June 2023, International Union of Crystallography

    Dr Pavel Afonine

  5. New tools for the analysis and validation of cryo-EM maps and atomic models

    Article • Acta Crystallographica Section D Structural Biology, September 2018, International Union of Crystallography

    Dr Pavel Afonine

  6. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation

    Article • Acta Crystallographica Section D Structural Biology, June 2018, International Union of Crystallography

    Dr Pavel Afonine

  7. Real-space refinement inPHENIXfor cryo-EM and crystallography

    Article • Acta Crystallographica Section D Structural Biology, May 2018, International Union of Crystallography

    Dr Pavel Afonine

  8. Solving the scalability issue in quantum-based refinement: Q|R#1

    Article • Acta Crystallographica Section D Structural Biology, November 2017, International Union of Crystallography

    Dr Pavel Afonine

  9. FEM: feature-enhanced map

    Article • Acta Crystallographica Section D Biological Crystallography, February 2015, International Union of Crystallography

    Dr Pavel Afonine

  10. From deep TLS validation to ensembles of atomic models built from elemental motions

    Article • January 2015, Cold Spring Harbor Laboratory Press

    Dr Pavel Afonine

  11. Predicting X-ray Diffuse Scattering from Translation Libration Screw Structural Ensembles

    Article • January 2015, Cold Spring Harbor Laboratory Press

    Dr Pavel Afonine

  12. Metrics for comparison of crystallographic maps

    Article • Acta Crystallographica Section D Biological Crystallography, September 2014, International Union of Crystallography

    Dr Pavel Afonine, Professor Vladimir Y. Lunin

  13. Virus model of brome mosaic virus (second half data set)

    Article • September 2014, Protein Data Bank, Rutgers University

    Dr Pavel Afonine

  14. Full virus map of brome mosaic virus

    Article • September 2014, Protein Data Bank, Rutgers University

    Dr Pavel Afonine

  15. Virus model of brome mosaic virus (first half data set)

    Article • September 2014, Protein Data Bank, Rutgers University

    Dr Pavel Afonine

  16. An atomic model of brome mosaic virus using direct electron detection and real-space optimization

    Article • Nature Communications, September 2014, Springer Science + Business Media

    Dr Pavel Afonine

  17. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

    Article • Acta Crystallographica Section D Biological Crystallography, April 2014, International Union of Crystallography

    Dr Pavel Afonine

  18. Automated identification of elemental ions in macromolecular crystal structures

    Article • Acta Crystallographica Section D Biological Crystallography, March 2014, International Union of Crystallography

    Dr Pavel Afonine

  19. Automating crystallographic structure solution and refinement of protein–ligand complexes

    Article • Acta Crystallographica Section D Biological Crystallography, December 2013, International Union of Crystallography

    Dr Pavel Afonine

  20. Improved Crystallographic Structures Using Extensive Combinatorial Refinement

    Article • Structure, November 2013, Elsevier

    Dr Pavel Afonine

  21. Model morphing and sequence assignment after molecular replacement

    Article • Acta Crystallographica Section D Biological Crystallography, October 2013, International Union of Crystallography

    Dr Pavel Afonine

  22. TLSfrom fundamentals to practice

    Article • Crystallography Reviews, October 2013, Taylor & Francis

    Dr Pavel Afonine

  23. Validated Near-Atomic Resolution Structure of Bacteriophage Epsilon15 Derived from Cryo-EM and Modeling

    Article • July 2013, Protein Data Bank, Rutgers University

    Dr Pavel Afonine

  24. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

    Article • Proceedings of the National Academy of Sciences, July 2013, Proceedings of the National Academy of Sciences

    Dr Pavel Afonine

  25. Bulk-solvent and overall scaling revisited: faster calculations, improved results

    Article • Acta Crystallographica Section D Biological Crystallography, March 2013, International Union of Crystallography

    Dr Pavel Afonine

  26. Crystallographic Maps and Models at Low and at Subatomic Resolutions

    Article • January 2013, Springer Science + Business Media

    Dr Pavel Afonine

  27. Crystallographic Structure Refinement in a Nutshell

    Article • January 2013, Springer Science + Business Media

    Dr Pavel Afonine

  28. Modelling dynamics in protein crystal structures by ensemble refinement

    Article • eLife, December 2012, eLife

    Dr Pavel Afonine

  29. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

    Article • Acta Crystallographica Section D Biological Crystallography, June 2012, International Union of Crystallography

    Dr Pavel Afonine

  30. Graphical tools for macromolecular crystallography inPHENIX

    Article • Journal of Applied Crystallography, May 2012, International Union of Crystallography

    Dr Pavel Afonine

  31. PHENIX: a comprehensive Python-based system for macromolecular structure solution

    Article • April 2012, International Union of Crystallography

    Dr Pavel Afonine

  32. Towards automated crystallographic structure refinement with phenix.refine

    Article • Acta Crystallographica Section D Biological Crystallography, March 2012, International Union of Crystallography

    Dr Pavel Afonine

  33. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

    Article • Acta Crystallographica Section D Biological Crystallography, March 2012, International Union of Crystallography

    Dr Pavel Afonine

  34. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta

    Article • Journal of Structural and Functional Genomics, March 2012, Springer Science + Business Media

    Dr Pavel Afonine

  35. The Phenix software for automated determination of macromolecular structures

    Article • Methods, September 2011, Elsevier

    Dr Pavel Afonine

  36. N-{N-[2-(3,5-Difluorophenyl)acetyl]-(S)-alanyl}-(S)-phenylglycinetert-butyl ester (DAPT): an inhibitor of γ-secretase, revealing fine electronic and hydrogen-bonding features

    Article • Acta Crystallographica Section C Crystal Structure Communications, November 2010, International Union of Crystallography

    Dr Pavel Afonine

  37. Joint X-ray and neutron refinement withphenix.refine

    Article • Acta Crystallographica Section D Biological Crystallography, October 2010, International Union of Crystallography

    Dr Pavel Afonine

  38. Coupling of receptor conformation and ligand orientation determine graded activity

    Article • Nature Chemical Biology, October 2010, Springer Science + Business Media

    Dr Pavel Afonine

  39. Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles

    Article • PLoS Computational Biology, August 2010, PLOS

    Dr Pavel Afonine

  40. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

    Article • Journal of Applied Crystallography, May 2010, International Union of Crystallography

    Dr Pavel Afonine

  41. Neutron Diffraction Studies of a Class A β-Lactamase Toho-1 E166A/R274N/R276N Triple Mutant

    Article • Journal of Molecular Biology, March 2010, Elsevier

    Dr Pavel Afonine, Dr Matthew P Blakeley

  42. PHENIX: a comprehensive Python-based system for macromolecular structure solution

    Article • Acta Crystallographica Section D Biological Crystallography, January 2010, International Union of Crystallography

    Dr Pavel Afonine

  43. On the use of logarithmic scales for analysis of diffraction data

    Article • Acta Crystallographica Section D Biological Crystallography, November 2009, International Union of Crystallography

    Dr Pavel Afonine

  44. Recent developments in phasing and structure refinement for macromolecular crystallography

    Article • Current Opinion in Structural Biology, October 2009, Elsevier

    Dr Pavel Afonine

  45. Averaged kick maps: less noise, more signal…and probably less bias

    Article • Acta Crystallographica Section D Biological Crystallography, August 2009, International Union of Crystallography

    Professor Dusan Turk, Dr Pavel Afonine

  46. Automatic multiple-zone rigid-body refinement with a large convergence radius

    Article • Journal of Applied Crystallography, July 2009, International Union of Crystallography

    Dr Pavel Afonine

  47. Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules

    Article • Acta Crystallographica Section D Biological Crystallography, May 2009, International Union of Crystallography

    Dr Pavel Afonine

  48. Decision-making in structure solution using Bayesian estimates of map quality: thePHENIX AutoSolwizard

    Article • Acta Crystallographica Section D Biological Crystallography, May 2009, International Union of Crystallography

    Dr Pavel Afonine

  49. Crystallographic model quality at a glance

    Article • Acta Crystallographica Section D Biological Crystallography, February 2009, International Union of Crystallography

    Dr Pavel Afonine

  50. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias

    Article • Acta Crystallographica Section D Biological Crystallography, April 2008, International Union of Crystallography

    Dr Pavel Afonine

  51. Protein structures by spallation neutron crystallography

    Article • Journal of Synchrotron Radiation, April 2008, International Union of Crystallography

    Dr Pavel Afonine

  52. Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase

    Article • Proceedings of the National Academy of Sciences, February 2008, Proceedings of the National Academy of Sciences

    Dr Pavel Afonine, Dr Matthew P Blakeley

  53. Automated Structure Solution with the PHENIX Suite

    Article • January 2008, Springer Science + Business Media

    Dr Pavel Afonine

  54. Iterative model building, structure refinement and density modification with thePHENIX AutoBuildwizard

    Article • Acta Crystallographica Section D Biological Crystallography, December 2007, International Union of Crystallography

    Dr Pavel Afonine

  55. On macromolecular refinement at subatomic resolution with interatomic scatterers

    Article • Acta Crystallographica Section D Biological Crystallography, October 2007, International Union of Crystallography

    Dr Pavel Afonine, Professor Vladimir Y. Lunin

  56. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

    Article • Acta Crystallographica Section D Biological Crystallography, April 2007, International Union of Crystallography

    Professor Dusan Turk, Dr Pavel Afonine

  57. Automated structure determination with phenix

    Article • January 2007, Springer Science + Business Media

    Dr Pavel Afonine

  58. A robust bulk solvent correction and anisotropic scaling procedure in the CCTBX

    Article • Acta Crystallographica Section A Foundations of Crystallography, August 2005, International Union of Crystallography

    Dr Pavel Afonine

  59. On the incompleteness of atomic models

    Article • Acta Crystallographica Section A Foundations of Crystallography, August 2005, International Union of Crystallography

    Dr Pavel Afonine

  60. Hybrid programming in crystallography: Phenix.refine and Phenix.hyss

    Article • Acta Crystallographica Section A Foundations of Crystallography, August 2005, International Union of Crystallography

    Dr Pavel Afonine

  61. A robust bulk-solvent correction and anisotropic scaling procedure

    Article • Acta Crystallographica Section D Biological Crystallography, June 2005, International Union of Crystallography

    Dr Pavel Afonine

  62. Some Applications of Dummy Point Scatterers for Phasing in Macromolecular X-Ray Crystallography

    Article • January 2005, Springer Science + Business Media

    Dr Pavel Afonine, Professor Vladimir Y. Lunin

  63. On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps

    Article • Acta Crystallographica Section D Biological Crystallography, January 2004, International Union of Crystallography

    Dr Pavel Afonine, Professor Vladimir Y. Lunin

  64. On a fast calculation of structure factors at a subatomic resolution

    Article • Acta Crystallographica Section A Foundations of Crystallography, December 2003, International Union of Crystallography

    Dr Pavel Afonine

  65. MLMF: least-squares approximation of likelihood-based refinement criteria

    Article • Journal of Applied Crystallography, January 2003, International Union of Crystallography

    Dr Pavel Afonine, Professor Vladimir Y. Lunin

  66. Quadratic approximation of the maximum-likelihood criterion

    Article • Acta Crystallographica Section A Foundations of Crystallography, August 2002, International Union of Crystallography

    Dr Pavel Afonine

  67. Likelihood-based refinement. I. Irremovable model errors

    Article • Acta Crystallographica Section A Foundations of Crystallography, May 2002, International Union of Crystallography

    Dr Pavel Afonine, Professor Vladimir Y. Lunin