Difference between revisions of "Publications"

From Phaserwiki
(→‎Primary Citations: Bringing up to date)
 
(40 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
Clicking on a paper title below will either get the PDF directly from this site, as allowed by certain journals, or will link you to the publisher's site (references flagged by an asterisk). Depending on the journal and your institution's licenses, you may or may not be able to access papers from publishers' sites. In such cases, links are given if possible to the abstract,
+
==Citation==
 +
;Phaser crystallographic software [https://scripts.iucr.org/cgi-bin/paper?he5368 '''J Appl Cryst''']
 +
:McCoy AJ, Grosse-Kunstleve RW,  Adams PD, Winn MD, Storoni LC, Read RJ
 +
:J. Appl. Cryst. (2007). 40, 658-674
  
−
{|
+
==Reviews==
−
|-
+
;Using SAD data in Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5159 '''Acta Cryst D''']
−
| [[Image:PDF_download.png | File:He5368.pdf‎]]
+
:Read RJ, McCoy AJ
−
|
+
:Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344
−
; Phaser crystallographic software
+
 
−
:J. Appl. Cryst. (2007). 40, 658-674
+
;Experimental phasing<nowiki>:</nowiki> best practice and pitfalls [https://scripts.iucr.org/cgi-bin/paper?ba5142 '''Acta Cryst D''']
−
:A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L.C. Storoni, R.J. Read.
+
:McCoy AJ, Read RJ
−
|-
+
:Acta Cryst. (2010) D66, 458-469.
−
| [[Image:PDF_download.png | File:Ba5095.pdf‎]]
+
 
−
|
+
;An introduction to molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5108 '''Acta Cryst D''']
−
; Solving structures of protein complexes by molecular replacement with Phaser
+
:Evans P, McCoy A
 +
:Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.
 +
 
 +
;Solving structures of protein complexes by molecular replacement with Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5095  '''Acta Cryst D''']
 +
:McCoy AJ
 
:Acta Cryst. (2007). D63, 32-41
 
:Acta Cryst. (2007). D63, 32-41
−
:A. J. McCoy
+
 
−
|-
+
;Liking Likelihood [https://scripts.iucr.org/cgi-bin/paper?ba5064 '''Acta Cryst D''']
−
| [[Image:PDF_download.png | File:Gx5042.pdf‎]]
+
:McCoy AJ
−
|
+
:Acta Cryst. (2004). D60, 2169-2183
−
; Likelihood-enhanced fast translation functions
+
 
 +
==Primary Citations==
 +
 
 +
;Likelihood-based interactive local docking into cryo-EM maps in ChimeraX [https://doi.org/10.1107/S2059798324006776 '''Acta Cryst D''']
 +
:Read RJ, Pettersen EF, McCoy AJ, Croll TI, Terwilliger TC, Poon BK, Meng EC, Liebschner D, Adams PD
 +
:Acta Cryst. (2024). D80, 588-598
 +
 
 +
;Likelihood-based docking of models into cryo-EM maps [https://doi.org/10.1107/S2059798323001602 '''Acta Cryst D''']
 +
:Mill&aacute;n C, McCoy AJ, Terwilliger TC, Read RJ
 +
:Acta Cryst. (2023). D79, 281-289
 +
 
 +
;Likelihood-based signal and noise analysis for docking of models into cryo-EM maps [https://doi.org/10.1107/S2059798323001596 '''Acta Cryst D''']
 +
:Read RJ, Mill&aacute;n C, McCoy AJ, Terwilliger TC
 +
:Acta Cryst. (2023). D79, 271-280.
 +
 
 +
;Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE [https://doi.org/10.1107/S2059798322010026 '''Acta Cryst D''']
 +
:Oeffner RD, Croll TI, Mill&aacute;n C, Poon BK, Schlicksup CJ, Read RJ, Terwilliger TC
 +
:Acta Cryst. (2022). D78, 1303-1314
 +
 
 +
;Implications of AlphaFold2 for crystallographic phasing by molecular replacement [https://doi.org/10.1107/S2059798321012122 '''Acta Cryst D''']
 +
:McCoy AJ, Sammito MD, Read RJ
 +
:Acta Cryst. (2022). D78, 1-13
 +
 
 +
;Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data [https://doi.org/10.1107/S2059798321004538 '''Acta Cryst D''']
 +
:Hatti KS, McCoy AJ, Read RJ
 +
:Acta Cryst. (2021). D77, 880-893
 +
 
 +
;Detection of translational noncrystallographic symmetry in Patterson functions [https://doi.org/10.1107/S2059798320016836 '''Acta Cryst D''']
 +
:Caballero I, Sammito MD, Afonine PV, Us&oacute;n I, Read RJ, McCoy AJ
 +
:Acta Cryst. (2021). D77, 131-141
 +
 
 +
;Phasertng&#58; directed acyclic graphs for crystallographic phasing [https://doi.org/10.1107/S2059798320014746 '''Acta Cryst D''']
 +
:McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ
 +
:Acta Cryst. (2021). D77, 1-10
 +
 
 +
;Measuring and using information gained by observing diffraction data [https://doi.org/10.1107/S2059798320001588 '''Acta Cryst D''']
 +
:Read RJ, Oeffner RD, McCoy AJ
 +
:Acta Cryst. (2020). D76, 238-247
 +
 
 +
;Factors influencing estimates of coordinate error for molecular replacement [https://doi.org/10.1107/S2059798319015730 '''Acta Cryst D''']
 +
:Hatti KS, McCoy AJ, Oeffner RD, Sammito MD, Read RJ
 +
:Acta Cryst. (2020). D76, 19-27
 +
 
 +
;Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with Phaser&#58; human Rab27a [https://doi.org/10.1107/S2059798318017825 '''Acta Cryst D''']
 +
:Jamshidiha M, P&eacute;rez-Dorado I, Murray JW, Tate EW, Cota E, Read RJ
 +
:Acta Cryst. (2019). D75, 342-353
 +
 
 +
;Gyre and gimble&#58; a maximum-likelihood replacement for Patterson correlation refinement [https://scripts.iucr.org/cgi-bin/paper?cb5100 '''Acta Cryst D''']
 +
:McCoy AJ, Oeffner RD, Mill&aacute;n, Sammito M, Us&oacute;n, Read RJ
 +
:Acta Cryst. (2018). D74, 279-289
 +
 
 +
;On the application of the expected log-likelihood gain to decision making in molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5282 '''Acta Cryst D''']
 +
:Oeffner RD, Afonine PV, Mill&aacute;n C, Sammito M, Us&oacute;n I, Read RJ, McCoy AJ
 +
:Acta Cryst. (2018). D74, 245-255
 +
 
 +
;Maximum-likelihood determination of anomalous substructures [https://scripts.iucr.org/cgi-bin/paper?ba5273 '''Acta Cryst D''']
 +
:Read RJ and McCoy AJ
 +
:Acta Cryst. (2018). D74, 89-105
 +
 
 +
;Ab initio solution of macromolecular crystal structures without direct methods [https://www.pnas.org/content/pnas/114/14/3637.full.pdf '''PNAS''']
 +
:McCoy AJ, Oeffner RD, Wrobel AG, Ojala JRM, Tryggvason K, Lohkamp B, Read RJ
 +
:Proc. Natl. Acad. Sci. USA (2017). 114, 3637-3641
 +
 
 +
;A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error [https://scripts.iucr.org/cgi-bin/paper?dz5382 '''Acta Cryst D''']
 +
:Read RJ, McCoy AJ
 +
:Acta Cryst. (2016). D72, 375-387
 +
 
 +
;Phaser.MRage&#58; automated molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5210 '''Acta Cryst D''']
 +
:Bunkoczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ
 +
:Acta Cryst. (2013). D69, 2276-2286
 +
 
 +
;SCEDS&#58; protein fragments for molecular replacement in Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5209 '''Acta Cryst D''']
 +
:McCoy AJ, Nicholls RA, Schneider TR
 +
:Acta Cryst. (2013). D69, 2216-2225
 +
 
 +
;Improved estimates of coordinate error for molecular replacement [https://scripts.iucr.org/cgi-bin/paper?ba5212 '''Acta Cryst D''']
 +
:Oeffner RD, Bunkocz G, McCoy AJ, Read RJ
 +
:Acta Cryst. (2013). D69, 2209-2215
 +
 
 +
;Intensity statistics in the presence of translational non-crystallographic symmetry [https://scripts.iucr.org/cgi-bin/paper?dz5268 '''Acta Cryst D''']
 +
:Read RJ, Adams PD, McCoy AJ
 +
:Acta Cryst. (2013). D69, 176-183
 +
 
 +
;Improvement of molecular replacement models with ''Sculptor'' [https://scripts.iucr.org/cgi-bin/paper?ba5163 '''Acta Cryst D''']
 +
:Bunkoczi G, Read RJ
 +
:Acta Cryst. (2011). D67, 303-312
 +
 
 +
;Likelihood-enhanced fast translation functions [https://scripts.iucr.org/cgi-bin/paper?gx5042 '''Acta Cryst D''']
 +
:McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ
 
:Acta Cryst. (2005). D61, 458-464
 
:Acta Cryst. (2005). D61, 458-464
−
:A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni, R. J. Read.
+
 
−
|-
+
;Simple algorithm for a maximum-likelihood SAD function [https://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D''']
−
| [[Image:PDF_download.png | File:Ba5064.pdf‎]]
+
:McCoy AJ, Storoni LC,  Read RJ
−
|
 
−
; Liking Likelihood
 
−
:Acta Cryst. (2004). D60, 2169-2183
 
−
:A. J. McCoy
 
−
|-
 
−
| [[Image:PDF.png | File:He5368.pdf‎]]
 
−
|
 
−
; Simple algorithm for a maximum-likelihood SAD function
 
 
:Acta Cryst. (2004). D60, 1220-1228
 
:Acta Cryst. (2004). D60, 1220-1228
−
:A. J. McCoy, L. C. Storoni, R. J. Read.
+
 
−
|-
+
;Likelihood-enhanced fast rotation functions [https://scripts.iucr.org/cgi-bin/paper?ad5007 '''Acta Cryst D'''] [http://www-structmed.cimr.cam.ac.uk/Personal/randy/pubs/ad5007.pdf '''pdf''']
−
| [[Image:PDF.png | File:Gx5042.pdf‎]]
+
:Storoni LC, McCoy AJ, Read RJ
−
|
 
−
; Likelihood-enhanced fast rotation functions
 
 
:Acta Cryst. (2004). D60, 432-438
 
:Acta Cryst. (2004). D60, 432-438
−
:L. C. Storoni, A. J. McCoy, R. J. Read.
+
 
−
|-
+
;Pushing the boundaries of molecular replacement with maximum likelihood [https://scripts.iucr.org/cgi-bin/paper?ba5014 '''Acta Cryst D''']
−
| [[Image:PDF.png | File:He5368.pdf‎]]
+
:Read RJ
−
|
 
−
; Pushing the boundaries of molecular replacement with maximum likelihood
 
 
:Acta Cryst. (2001). D57, 1373-1382
 
:Acta Cryst. (2001). D57, 1373-1382
−
:R. J. Read.
 
−
|}
 

Latest revision as of 14:54, 24 November 2025

Citation

Phaser crystallographic software J Appl Cryst
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ
J. Appl. Cryst. (2007). 40, 658-674

Reviews

Using SAD data in Phaser Acta Cryst D
Read RJ, McCoy AJ
Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):338-344
Experimental phasing: best practice and pitfalls Acta Cryst D
McCoy AJ, Read RJ
Acta Cryst. (2010) D66, 458-469.
An introduction to molecular replacement Acta Cryst D
Evans P, McCoy A
Acta Cryst.(2008) D64, 1-10. Epub 2007 Dec 5.
Solving structures of protein complexes by molecular replacement with Phaser Acta Cryst D
McCoy AJ
Acta Cryst. (2007). D63, 32-41
Liking Likelihood Acta Cryst D
McCoy AJ
Acta Cryst. (2004). D60, 2169-2183

Primary Citations

Likelihood-based interactive local docking into cryo-EM maps in ChimeraX Acta Cryst D
Read RJ, Pettersen EF, McCoy AJ, Croll TI, Terwilliger TC, Poon BK, Meng EC, Liebschner D, Adams PD
Acta Cryst. (2024). D80, 588-598
Likelihood-based docking of models into cryo-EM maps Acta Cryst D
Millán C, McCoy AJ, Terwilliger TC, Read RJ
Acta Cryst. (2023). D79, 281-289
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps Acta Cryst D
Read RJ, Millán C, McCoy AJ, Terwilliger TC
Acta Cryst. (2023). D79, 271-280.
Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE Acta Cryst D
Oeffner RD, Croll TI, Millán C, Poon BK, Schlicksup CJ, Read RJ, Terwilliger TC
Acta Cryst. (2022). D78, 1303-1314
Implications of AlphaFold2 for crystallographic phasing by molecular replacement Acta Cryst D
McCoy AJ, Sammito MD, Read RJ
Acta Cryst. (2022). D78, 1-13
Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data Acta Cryst D
Hatti KS, McCoy AJ, Read RJ
Acta Cryst. (2021). D77, 880-893
Detection of translational noncrystallographic symmetry in Patterson functions Acta Cryst D
Caballero I, Sammito MD, Afonine PV, Usón I, Read RJ, McCoy AJ
Acta Cryst. (2021). D77, 131-141
Phasertng: directed acyclic graphs for crystallographic phasing Acta Cryst D
McCoy AJ, Stockwell DH, Sammito MD, Oeffner RD, Hatti KS, Croll TI, Read RJ
Acta Cryst. (2021). D77, 1-10
Measuring and using information gained by observing diffraction data Acta Cryst D
Read RJ, Oeffner RD, McCoy AJ
Acta Cryst. (2020). D76, 238-247
Factors influencing estimates of coordinate error for molecular replacement Acta Cryst D
Hatti KS, McCoy AJ, Oeffner RD, Sammito MD, Read RJ
Acta Cryst. (2020). D76, 19-27
Coping with strong translational non-crystallographic symmetry and extreme anisotropy in molecular replacement with Phaser: human Rab27a Acta Cryst D
Jamshidiha M, Pérez-Dorado I, Murray JW, Tate EW, Cota E, Read RJ
Acta Cryst. (2019). D75, 342-353
Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement Acta Cryst D
McCoy AJ, Oeffner RD, Millán, Sammito M, Usón, Read RJ
Acta Cryst. (2018). D74, 279-289
On the application of the expected log-likelihood gain to decision making in molecular replacement Acta Cryst D
Oeffner RD, Afonine PV, Millán C, Sammito M, Usón I, Read RJ, McCoy AJ
Acta Cryst. (2018). D74, 245-255
Maximum-likelihood determination of anomalous substructures Acta Cryst D
Read RJ and McCoy AJ
Acta Cryst. (2018). D74, 89-105
Ab initio solution of macromolecular crystal structures without direct methods PNAS
McCoy AJ, Oeffner RD, Wrobel AG, Ojala JRM, Tryggvason K, Lohkamp B, Read RJ
Proc. Natl. Acad. Sci. USA (2017). 114, 3637-3641
A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error Acta Cryst D
Read RJ, McCoy AJ
Acta Cryst. (2016). D72, 375-387
Phaser.MRage: automated molecular replacement Acta Cryst D
Bunkoczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ
Acta Cryst. (2013). D69, 2276-2286
SCEDS: protein fragments for molecular replacement in Phaser Acta Cryst D
McCoy AJ, Nicholls RA, Schneider TR
Acta Cryst. (2013). D69, 2216-2225
Improved estimates of coordinate error for molecular replacement Acta Cryst D
Oeffner RD, Bunkocz G, McCoy AJ, Read RJ
Acta Cryst. (2013). D69, 2209-2215
Intensity statistics in the presence of translational non-crystallographic symmetry Acta Cryst D
Read RJ, Adams PD, McCoy AJ
Acta Cryst. (2013). D69, 176-183
Improvement of molecular replacement models with Sculptor Acta Cryst D
Bunkoczi G, Read RJ
Acta Cryst. (2011). D67, 303-312
Likelihood-enhanced fast translation functions Acta Cryst D
McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ
Acta Cryst. (2005). D61, 458-464
Simple algorithm for a maximum-likelihood SAD function Acta Cryst D
McCoy AJ, Storoni LC, Read RJ
Acta Cryst. (2004). D60, 1220-1228
Likelihood-enhanced fast rotation functions Acta Cryst D pdf
Storoni LC, McCoy AJ, Read RJ
Acta Cryst. (2004). D60, 432-438
Pushing the boundaries of molecular replacement with maximum likelihood Acta Cryst D
Read RJ
Acta Cryst. (2001). D57, 1373-1382
Retrieved from "https://www.phaser.cimr.cam.ac.uk/index.php?title=Publications&oldid=2528"