skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on October 1, 2020

Title: Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix

Authors:
ORCiD logo [1]; ORCiD logo [1];  [2];  [2];  [3];  [4];  [5];  [4];  [5];  [5];  [4];  [2];  [4];  [2];  [5];  [4];  [5];  [5];  [4];  [2] more »;  [4];  [6];  [5];  [5];  [2] « less
  1. Los Alamos National Laboratory
  2. Lawrence Berkeley National Laboratory
  3. Baylor College of Medicine
  4. University of Cambridge
  5. Duke University
  6. Centre for Integrative Biology, France
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1597368
Report Number(s):
LA-UR-19-31498
Journal ID: 2059-7983
Grant/Contract Number:  
89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Acta Crystallographica. Section D. Structural Biology
Additional Journal Information:
Journal Volume: 75; Journal Issue: 10
Country of Publication:
United States
Language:
English
Subject:
Biological Science

Citation Formats

Terwilliger, Thomas Charles, Hung, Li-Wei, Liebschner, Dorothee, Afonine, Pavel V, Baker, Matthew, Bunkoczi, Gabor, Chen, Vincent B, Croll, Tristan I, Hintze, Bradley, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D, Poon, Billy K., Prisant, Michael G, Read, Randy J., Richardson, Jane S, Richardson, David S, Sammito, Massimo D, Sobolev, Oleg V., Stockwell, Duncan H, Urzhumtsev, Alexandre, Videau, Lizbeth L, Williams, Christopher J, and Adams, Paul D. Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix. United States: N. p., 2019. Web. doi:10.1107/S2059798319011471.
Terwilliger, Thomas Charles, Hung, Li-Wei, Liebschner, Dorothee, Afonine, Pavel V, Baker, Matthew, Bunkoczi, Gabor, Chen, Vincent B, Croll, Tristan I, Hintze, Bradley, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D, Poon, Billy K., Prisant, Michael G, Read, Randy J., Richardson, Jane S, Richardson, David S, Sammito, Massimo D, Sobolev, Oleg V., Stockwell, Duncan H, Urzhumtsev, Alexandre, Videau, Lizbeth L, Williams, Christopher J, & Adams, Paul D. Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix. United States. doi:10.1107/S2059798319011471.
Terwilliger, Thomas Charles, Hung, Li-Wei, Liebschner, Dorothee, Afonine, Pavel V, Baker, Matthew, Bunkoczi, Gabor, Chen, Vincent B, Croll, Tristan I, Hintze, Bradley, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D, Poon, Billy K., Prisant, Michael G, Read, Randy J., Richardson, Jane S, Richardson, David S, Sammito, Massimo D, Sobolev, Oleg V., Stockwell, Duncan H, Urzhumtsev, Alexandre, Videau, Lizbeth L, Williams, Christopher J, and Adams, Paul D. Tue . "Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix". United States. doi:10.1107/S2059798319011471.
@article{osti_1597368,
title = {Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix},
author = {Terwilliger, Thomas Charles and Hung, Li-Wei and Liebschner, Dorothee and Afonine, Pavel V and Baker, Matthew and Bunkoczi, Gabor and Chen, Vincent B and Croll, Tristan I and Hintze, Bradley and Jain, Swati and McCoy, Airlie J. and Moriarty, Nigel W. and Oeffner, Robert D and Poon, Billy K. and Prisant, Michael G and Read, Randy J. and Richardson, Jane S and Richardson, David S and Sammito, Massimo D and Sobolev, Oleg V. and Stockwell, Duncan H and Urzhumtsev, Alexandre and Videau, Lizbeth L and Williams, Christopher J and Adams, Paul D.},
abstractNote = {},
doi = {10.1107/S2059798319011471},
journal = {Acta Crystallographica. Section D. Structural Biology},
number = 10,
volume = 75,
place = {United States},
year = {2019},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on October 1, 2020
Publisher's Version of Record

Save / Share:

Works referenced in this record:

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Recent developments in phasing and structure refinement for macromolecular crystallography
journal, October 2009

  • Adams, Paul D.; Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.
  • Current Opinion in Structural Biology, Vol. 19, Issue 5
  • DOI: 10.1016/j.sbi.2009.07.014

PHENIX : building new software for automated crystallographic structure determination
journal, October 2002

  • Adams, Paul D.; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
  • DOI: 10.1107/S0907444902016657

Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules
journal, May 2009

  • Adams, Paul D.; Mustyakimov, Marat; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
  • DOI: 10.1107/S0907444909011548

From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation
journal, June 2018

  • Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 7
  • DOI: 10.1107/S2059798318005764

A robust bulk-solvent correction and anisotropic scaling procedure
journal, June 2005

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 7
  • DOI: 10.1107/S0907444905007894

On macromolecular refinement at subatomic resolution with interatomic scatterers
journal, October 2007

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 11
  • DOI: 10.1107/S0907444907046148

Bulk-solvent and overall scaling revisited: faster calculations, improved results
journal, March 2013

  • Afonine, P. V.; Grosse-Kunstleve, R. W.; Adams, P. D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 4
  • DOI: 10.1107/S0907444913000462

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

Automatic multiple-zone rigid-body refinement with a large convergence radius
journal, July 2009

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Urzhumtsev, Alexandre
  • Journal of Applied Crystallography, Vol. 42, Issue 4
  • DOI: 10.1107/S0021889809023528

New tools for the analysis and validation of cryo-EM maps and atomic models
journal, September 2018

  • Afonine, Pavel V.; Klaholz, Bruno P.; Moriarty, Nigel W.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 9
  • DOI: 10.1107/S2059798318009324

FEM: feature-enhanced map
journal, February 2015

  • Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 3
  • DOI: 10.1107/S1399004714028132

Joint X-ray and neutron refinement with phenix.refine
journal, October 2010

  • Afonine, Pavel V.; Mustyakimov, Marat; Grosse-Kunstleve, Ralf W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 11
  • DOI: 10.1107/S0907444910026582

Real-space refinement in PHENIX for cryo-EM and crystallography
journal, May 2018

  • Afonine, Pavel V.; Poon, Billy K.; Read, Randy J.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318006551

How cryo-EM is revolutionizing structural biology
journal, January 2015

  • Bai, Xiao-chen; McMullan, Greg; Scheres, Sjors H. W.
  • Trends in Biochemical Sciences, Vol. 40, Issue 1
  • DOI: 10.1016/j.tibs.2014.10.005

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy
journal, August 2015

  • Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei
  • Nature Methods, Vol. 12, Issue 10
  • DOI: 10.1038/nmeth.3541

Conformation Dependence of Backbone Geometry in Proteins
journal, October 2009


The protein data bank: A computer-based archival file for macromolecular structures
journal, May 1977

  • Bernstein, Frances C.; Koetzle, Thomas F.; Williams, Graheme J. B.
  • Journal of Molecular Biology, Vol. 112, Issue 3
  • DOI: 10.1016/S0022-2836(77)80200-3

Between objectivity and subjectivity
journal, February 1990

  • Bränd´en, Carl-Ivar; Alwyn Jones, T.
  • Nature, Vol. 343, Issue 6260
  • DOI: 10.1038/343687a0

Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
journal, January 1992


Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
journal, September 1998

  • Brünger, A. T.; Adams, P. D.; Clore, G. M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 54, Issue 5
  • DOI: 10.1107/S0907444998003254

Neutron diffraction studies towards deciphering the protonation state of catalytic residues in the bacterial KDN9P phosphatase
journal, August 2013

  • Bryan, Tyrel; González, Javier M.; Bacik, John P.
  • Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 69, Issue 9
  • DOI: 10.1107/S1744309113021386

Phaser.MRage : automated molecular replacement
journal, October 2013

  • Bunkóczi, Gábor; Echols, Nathaniel; McCoy, Airlie J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 11
  • DOI: 10.1107/S0907444913022750

Improvement of molecular-replacement models with Sculptor
journal, March 2011

  • Bunkóczi, Gábor; Read, Randy J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910051218

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
journal, October 2018

  • Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky1004

Modelling dynamics in protein crystal structures by ensemble refinement
journal, December 2012


One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions
journal, November 2013

  • Cardone, Giovanni; Heymann, J. Bernard; Steven, Alasdair C.
  • Journal of Structural Biology, Vol. 184, Issue 2
  • DOI: 10.1016/j.jsb.2013.08.002

Femtosecond X-ray protein nanocrystallography
journal, February 2011

  • Chapman, Henry N.; Fromme, Petra; Barty, Anton
  • Nature, Vol. 470, Issue 7332, p. 73-77
  • DOI: 10.1038/nature09750

De Novo modeling in cryo-EM density maps with Pathwalking
journal, December 2016

  • Chen, Muyuan; Baldwin, Philip R.; Ludtke, Steven J.
  • Journal of Structural Biology, Vol. 196, Issue 3
  • DOI: 10.1016/j.jsb.2016.06.004

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
journal, November 2009

  • Chen, Vincent B.; Davis, Ian W.; Richardson, David C.
  • Protein Science, Vol. 18, Issue 11
  • DOI: 10.1002/pro.250

Correcting pervasive errors in RNA crystallography through enumerative structure prediction
journal, December 2012

  • Chou, Fang-Chieh; Sripakdeevong, Parin; Dibrov, Sergey M.
  • Nature Methods, Vol. 10, Issue 1
  • DOI: 10.1038/nmeth.2262

Comparative X-Ray and Neutron Diffraction Study of Bonding Effects in s-Triazine
journal, December 1967


Improved low-resolution crystallographic refinement with Phenix and Rosetta
journal, September 2013

  • DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J.
  • Nature Methods, Vol. 10, Issue 11
  • DOI: 10.1038/nmeth.2648

Improved molecular replacement by density- and energy-guided protein structure optimization
journal, May 2011

  • DiMaio, Frank; Terwilliger, Thomas C.; Read, Randy J.
  • Nature, Vol. 473, Issue 7348
  • DOI: 10.1038/nature09964

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Accurate bond and angle parameters for X-ray protein structure refinement
journal, July 1991

  • Engh, R. A.; Huber, R.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 4
  • DOI: 10.1107/S0108767391001071

An introduction to stereochemical restraints
journal, December 2006

  • Evans, Philip R.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1
  • DOI: 10.1107/S090744490604604X

An introduction to molecular replacement
journal, December 2007

  • Evans, Philip; McCoy, Airlie
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S0907444907051554

Geometric Parameters in Nucleic Acids:  Sugar and Phosphate Constituents
journal, January 1996

  • Gelbin, Anke; Schneider, Bohdan; Clowney, Lester
  • Journal of the American Chemical Society, Vol. 118, Issue 3
  • DOI: 10.1021/ja9528846

UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System
journal, September 2017

  • Goddard, Thomas D.; Huang, Conrad C.; Meng, Elaine C.
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3235

Substructure search procedures for macromolecular structures
journal, October 2003

  • Grosse-Kunstleve, R. W.; Adams, P. D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 11
  • DOI: 10.1107/S0907444903018043

The Computational Crystallography Toolbox : crystallographic algorithms in a reusable software framework
journal, January 2002

  • Grosse-Kunstleve, Ralf W.; Sauter, Nicholas K.; Moriarty, Nigel W.
  • Journal of Applied Crystallography, Vol. 35, Issue 1
  • DOI: 10.1107/S0021889801017824

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution
journal, March 2012

  • Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444911047834

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement
journal, April 2014

  • Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 5
  • DOI: 10.1107/S1399004714003277

Molprobity's ultimate rotamer-library distributions for model validation: MolProbity's Ultimate Rotamer-Library
journal, June 2016

  • Hintze, Bradley J.; Lewis, Steven M.; Richardson, Jane S.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 84, Issue 9
  • DOI: 10.1002/prot.25039

Matplotlib: A 2D Graphics Environment
journal, January 2007


Improved methods for building protein models in electron density maps and the location of errors in these models
journal, March 1991

  • Jones, T. A.; Zou, J. Y.; Cowan, S. W.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 2, p. 110-119
  • DOI: 10.1107/S0108767390010224

A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis
journal, March 1958

  • Kendrew, J. C.; Bodo, G.; Dintzis, H. M.
  • Nature, Vol. 181, Issue 4610, p. 662-666
  • DOI: 10.1038/181662a0

Checking your imagination: applications of the free R value
journal, August 1996


Where freedom is given, liberties are taken
journal, June 1995


Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate
journal, October 2015

  • Knihtila, Ryan; Holzapfel, Genevieve; Weiss, Kevin
  • Journal of Biological Chemistry, Vol. 290, Issue 52
  • DOI: 10.1074/jbc.M115.679860

Quantifying the local resolution of cryo-EM density maps
journal, November 2013

  • Kucukelbir, Alp; Sigworth, Fred J.; Tagare, Hemant D.
  • Nature Methods, Vol. 11, Issue 1
  • DOI: 10.1038/nmeth.2727

The Resolution Revolution
journal, March 2014


Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM
journal, May 2013

  • Li, Xueming; Mooney, Paul; Zheng, Shawn
  • Nature Methods, Vol. 10, Issue 6
  • DOI: 10.1038/nmeth.2472

Polder maps: improving OMIT maps by excluding bulk solvent
journal, February 2017

  • Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.
  • Acta Crystallographica Section D Structural Biology, Vol. 73, Issue 2, p. 148-157
  • DOI: 10.1107/S2059798316018210

Atomic resolution structure determination by the cryo-EM method MicroED: Atomic Resolution Structure Determination
journal, August 2016

  • Liu, Shian; Hattne, Johan; Reyes, Francis E.
  • Protein Science, Vol. 26, Issue 1
  • DOI: 10.1002/pro.2989

Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes
journal, October 2017

  • von Loeffelholz, Ottilie; Natchiar, S. Kundhavai; Djabeur, Nadia
  • Current Opinion in Structural Biology, Vol. 46
  • DOI: 10.1016/j.sbi.2017.07.007

Structure validation by Cα geometry: ϕ,ψ and Cβ deviation
journal, January 2003

  • Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan
  • Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3
  • DOI: 10.1002/prot.10286

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation
journal, September 2009

  • Moriarty, Nigel W.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 10
  • DOI: 10.1107/S0907444909029436

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
journal, June 2014

  • Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.
  • FEBS Journal, Vol. 281, Issue 18
  • DOI: 10.1111/febs.12860

A new default restraint library for the protein backbone in Phenix : a conformation-dependent geometry goes mainstream
journal, January 2016

  • Moriarty, Nigel W.; Tronrud, Dale E.; Adams, Paul D.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 1
  • DOI: 10.1107/S2059798315022408

Visualization of chemical modifications in the human 80S ribosome structure
journal, November 2017

  • Natchiar, S. Kundhavai; Myasnikov, Alexander G.; Kratzat, Hanna
  • Nature, Vol. 551, Issue 7681
  • DOI: 10.1038/nature24482

A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent
journal, January 2001

  • Oldfield, Thomas J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 1
  • DOI: 10.1107/S0907444900014098

Decacarbonyl-μ-hydrido-μ-vinyl- triangulo -triosmium: a combined X-ray and neutron diffraction study
journal, August 1978

  • Orpen, A. G.; Pippard, D.; Sheldrick, G. M.
  • Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 34, Issue 8
  • DOI: 10.1107/S0567740878014697

A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning
journal, June 2003

  • Padilla, Jennifer E.; Yeates, Todd O.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7
  • DOI: 10.1107/S0907444903007947

Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis
journal, February 1960

  • Perutz, M. F.; Rossmann, M. G.; Cullis, Ann F.
  • Nature, Vol. 185, Issue 4711
  • DOI: 10.1038/185416a0

A New Generation of Crystallographic Validation Tools for the Protein Data Bank
journal, October 2011


Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy
journal, October 2003


Serial crystallography using synchrotron radiation
journal, February 2014


Fast procedure for reconstruction of full-atom protein models from reduced representations
journal, January 2008

  • Rotkiewicz, Piotr; Skolnick, Jeffrey
  • Journal of Computational Chemistry, Vol. 29, Issue 9
  • DOI: 10.1002/jcc.20906

Serial femtosecond crystallography: the first five years
journal, February 2015


On the rigid-body motion of molecules in crystals
journal, January 1968

  • Schomaker, V.; Trueblood, K. N.
  • Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 24, Issue 1
  • DOI: 10.1107/S0567740868001718

A short history of SHELX
journal, December 2007

  • Sheldrick, George M.
  • Acta Crystallographica Section A Foundations of Crystallography, Vol. 64, Issue 1, p. 112-122
  • DOI: 10.1107/S0108767307043930

Programming new geometry restraints: parallelity of atomic groups
journal, July 2015

  • Sobolev, Oleg V.; Afonine, Pavel V.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 48, Issue 4
  • DOI: 10.1107/S1600576715010432

Serial crystallography at synchrotrons and X-ray lasers
journal, February 2017


Maximum-likelihood density modification
journal, August 2000

  • Terwilliger, Thomas C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 56, Issue 8
  • DOI: 10.1107/S0907444900005072

Automated structure solution, density modification and model building
journal, October 2002

  • Terwilliger, Thomas C.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 11
  • DOI: 10.1107/S0907444902016438

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018


Ligand identification using electron-density map correlations
journal, December 2006

  • Terwilliger, Thomas C.; Adams, Paul D.; Moriarty, Nigel W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 1
  • DOI: 10.1107/S0907444906046233

Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
journal, May 2009

  • Terwilliger, Thomas C.; Adams, Paul D.; Read, Randy J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 6
  • DOI: 10.1107/S0907444909012098

Automated MAD and MIR structure solution
journal, April 1999

  • Terwilliger, Thomas C.; Berendzen, Joel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 55, Issue 4
  • DOI: 10.1107/S0907444999000839

Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing
journal, March 2016

  • Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 3
  • DOI: 10.1107/S2059798315019269

Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal
journal, March 2016

  • Terwilliger, Thomas C.; Bunkóczi, Gábor; Hung, Li-Wei
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 3
  • DOI: 10.1107/S2059798315019403

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta
journal, March 2012

  • Terwilliger, Thomas C.; DiMaio, Frank; Read, Randy J.
  • Journal of Structural and Functional Genomics, Vol. 13, Issue 2
  • DOI: 10.1007/s10969-012-9129-3

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Automated ligand fitting by core-fragment fitting and extension into density
journal, July 2006

  • Terwilliger, Thomas C.; Klei, Herbert; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
  • DOI: 10.1107/S0907444906017161

Model morphing and sequence assignment after molecular replacement
journal, October 2013

  • Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 11
  • DOI: 10.1107/S0907444913017770

Automated map sharpening by maximization of detail and connectivity
journal, May 2018

  • Terwilliger, Thomas C.; Sobolev, Oleg V.; Afonine, Pavel V.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 6
  • DOI: 10.1107/S2059798318004655

Metrics for comparison of crystallographic maps
journal, September 2014

  • Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 10
  • DOI: 10.1107/S1399004714016289

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum
journal, August 2016

  • Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 9
  • DOI: 10.1107/S2059798316013048

Crystallographic model quality at a glance
journal, February 2009

  • Urzhumtseva, Ludmila; Afonine, Pavel V.; Adams, Paul D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 65, Issue 3
  • DOI: 10.1107/S0907444908044296

REFMAC 5 dictionary: organization of prior chemical knowledge and guidelines for its use
journal, November 2004

  • Vagin, Alexei A.; Steiner, Roberto A.; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12
  • DOI: 10.1107/S0907444904023510

Diffuse X-Ray Scattering to Model Protein Motions
journal, February 2014


Bringing diffuse X-ray scattering into focus
journal, June 2018

  • Wall, Michael E.; Wolff, Alexander M.; Fraser, James S.
  • Current Opinion in Structural Biology, Vol. 50
  • DOI: 10.1016/j.sbi.2018.01.009

MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG
journal, November 2017

  • Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W.
  • Protein Science, Vol. 27, Issue 1
  • DOI: 10.1002/pro.3330

Studies of ribonuclease-A by X-ray and neutron diffraction
journal, August 1980

  • Wlodawer, A.
  • Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, Vol. 36, Issue 8
  • DOI: 10.1107/S0567740880007315

A procedure for joint refinement of macromolecular structures with X-ray and neutron diffraction data from single crystals
journal, March 1982


Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms 1 1Edited by J. Thornton
journal, January 1999

  • Word, J. Michael; Lovell, Simon C.; LaBean, Thomas H.
  • Journal of Molecular Biology, Vol. 285, Issue 4
  • DOI: 10.1006/jmbi.1998.2400

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
journal, January 1999

  • Word, J. Michael; Lovell, Simon C.; Richardson, Jane S.
  • Journal of Molecular Biology, Vol. 285, Issue 4
  • DOI: 10.1006/jmbi.1998.2401

Low-barrier hydrogen bond in photoactive yellow protein
journal, January 2009

  • Yamaguchi, S.; Kamikubo, H.; Kurihara, K.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 2
  • DOI: 10.1073/pnas.0811882106

Anomalous signal indicators in protein crystallography
journal, October 2005