Difference between revisions of "Publications"
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==Primary Citations== | ==Primary Citations== | ||
− | ;A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error [ | + | ;Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement [https://scripts.iucr.org/cgi-bin/paper?cb5100 '''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 [https://scripts.iucr.org/cgi-bin/paper?ba5282 '''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 [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 | :Read RJ, McCoy AJ | ||
:Acta Cryst. (2016). D72, 375-387 | :Acta Cryst. (2016). D72, 375-387 | ||
− | ;Phaser.MRage: automated molecular replacement [ | + | ;Phaser.MRage: 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 | :Bunkoczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ | ||
:Acta Cryst. (2013). D69, 2276-2286 | :Acta Cryst. (2013). D69, 2276-2286 | ||
− | ;SCEDS: protein fragments for molecular replacement in Phaser [ | + | ;SCEDS: protein fragments for molecular replacement in Phaser [https://scripts.iucr.org/cgi-bin/paper?ba5209 '''Acta Cryst D'''] |
:McCoy AJ, Nicholls RA, Schneider TR | :McCoy AJ, Nicholls RA, Schneider TR | ||
:Acta Cryst. (2013). D69, 2216-2225 | :Acta Cryst. (2013). D69, 2216-2225 | ||
− | ;Improved estimates of coordinate error for molecular replacement [ | + | ;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 | :Oeffner RD, Bunkocz G, McCoy AJ, Read RJ | ||
:Acta Cryst. (2013). D69, 2209-2215 | :Acta Cryst. (2013). D69, 2209-2215 | ||
− | ;Intensity statistics in the presence of translational non-crystallographic symmetry [ | + | ;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 | :Read RJ, Adams PD, McCoy AJ | ||
:Acta Cryst. (2013). D69, 176-183 | :Acta Cryst. (2013). D69, 176-183 | ||
− | ;Improvement of molecular replacement models with ''Sculptor'' [ | + | ;Improvement of molecular replacement models with ''Sculptor'' [https://scripts.iucr.org/cgi-bin/paper?ba5163 '''Acta Cryst D'''] |
:Bunkoczi G, Read RJ | :Bunkoczi G, Read RJ | ||
:Acta Cryst. (2011). D67, 303-312 | :Acta Cryst. (2011). D67, 303-312 | ||
− | ;Likelihood-enhanced fast translation functions [ | + | ;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 | :McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ | ||
:Acta Cryst. (2005). D61, 458-464 | :Acta Cryst. (2005). D61, 458-464 | ||
− | ;Simple algorithm for a maximum-likelihood SAD function [ | + | ;Simple algorithm for a maximum-likelihood SAD function [https://scripts.iucr.org/cgi-bin/paper?ea5015 '''Acta Cryst D'''] |
:McCoy AJ, Storoni LC, Read RJ | :McCoy AJ, Storoni LC, Read RJ | ||
:Acta Cryst. (2004). D60, 1220-1228 | :Acta Cryst. (2004). D60, 1220-1228 | ||
− | ;Likelihood-enhanced fast rotation functions [ | + | ;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'''] |
:Storoni LC, McCoy AJ, Read RJ | :Storoni LC, McCoy AJ, Read RJ | ||
:Acta Cryst. (2004). D60, 432-438 | :Acta Cryst. (2004). D60, 432-438 | ||
− | ;Pushing the boundaries of molecular replacement with maximum likelihood [ | + | ;Pushing the boundaries of molecular replacement with maximum likelihood [https://scripts.iucr.org/cgi-bin/paper?ba5014 '''Acta Cryst D'''] |
:Read RJ | :Read RJ | ||
:Acta Cryst. (2001). D57, 1373-1382 | :Acta Cryst. (2001). D57, 1373-1382 |
Revision as of 17:24, 6 December 2018
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
- 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