The CCP4 suite: integrative software for macromolecular crystallography

Authors: Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Baslé, Arnaud, Beilsten-Edmands, James, Borges, Rafael J., Brown, David G., Burgos-Mármol, J. Javier, Berrisford, John M., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, Grzegorz, Cook, Atlanta G., Cowtan, Kevin D., Croll, Tristan I., Debreczeni, Judit É., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, Maria, Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Hoh, Soon Wen, Hough, Michael A., Jenkins, Huw T., Jiménez, Elisabet, Joosten, Robbie P., Keegan, Ronan M., Keep, Nicholas, Krissinel, Eugene B., Kolenko, Petr, Kovalevskiy, Oleg, Lamzin, Victor S., Lawson, David M., Lebedev, Andrey A., Leslie, Andrew G. W., Lohkamp, Bernhard, Long, Fei, Malý, Martin, McCoy, Airlie J., McNicholas, Stuart J., Medina, Ana, Millán, Claudia, Murray, James W., Murshudov, Garib N., Nicholls, Robert A., Noble, Martin E. M., Oeffner, Robert, Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, Daniel J., Rochira, William, Sammito, Massimo, Sánchez Rodríguez, Filomeno, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, Adam J., Skubak, Pavol, Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, Ivo, Thomas, Jens M. H., Thorn, Andrea, Valls, Josep Triviño, Uski, Ville, Usón, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, Marcin, Yamashita, Keitaro

Source: Acta crystallographica.Section D.Structural biology. 79(6):449-461

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100184496496.0x000001&indx=1&recIds=ETOCvdc_100184496496.0x000001

Likelihood‐based docking of models into cryo‐EM maps

Authors: Millán, Claudia, McCoy, Airlie J., Terwilliger, Thomas C., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 79(4):281-289

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181613679.0x000001&indx=1&recIds=ETOCvdc_100181613679.0x000001

Likelihood‐based signal and noise analysis for docking of models into cryo‐EM maps

Authors: Read, Randy J., Millán, Claudia, McCoy, Airlie J., Terwilliger, Thomas C.

Source: Acta crystallographica.Section D.Structural biology. 79(4):271-280

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100181613606.0x000001&indx=1&recIds=ETOCvdc_100181613606.0x000001

Accelerating crystal structure determination with iterative AlphaFold prediction

Authors: Terwilliger, Thomas C., Afonine, Pavel V., Liebschner, Dorothee, Croll, Tristan I., McCoy, Airlie J., Oeffner, Robert D., Williams, Christopher J., Poon, Billy K., Richardson, Jane S., Read, Randy J., Adams, Paul D.

Source: Acta crystallographica.Section D.Structural biology. 79(3):234-244

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100176921167.0x000001&indx=1&recIds=ETOCvdc_100176921167.0x000001

CRLF3 plays a key role in the final stage of platelet genesis and is a potential therapeutic target for thrombocythemia

Authors: Bennett, Cavan ^*, Lawrence, Moyra, Guerrero, Jose A., Stritt, Simon, Waller, Amie K., Yan, Yahui, Mifsud, Richard W., Ballester-Beltrán, Jose, Baig, Ayesha, Mueller, Annett, Mayer, Louisa, Warland, James, Penkett, Christopher J., Akbari, Parsa, Moreau, Thomas, Evans, Amanda L., Mookerjee, Souradip, Hoffman, Gary J., Saeb-Parsy, Kourosh, Adams, David J., Couzens, Amber L., Bender, Markus, Erber, Wendy N., Nieswandt, Bernhard, Read, Randy J., Ghevaert, Cedric ^**

Source: In Blood 7 April 2022 139(14):2227-2239

Implications of AlphaFold2 for crystallographic phasing by molecular replacement

Authors: McCoy, Airlie J., Sammito, Massimo D., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 78(1):1-13

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100138804295.0x000001&indx=1&recIds=ETOCvdc_100138804295.0x000001

Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE

Authors: Oeffner, Robert D., Croll, Tristan I., Millán, Claudia, Poon, Billy K., Schlicksup, Christopher J., Read, Randy J., Terwilliger, Tom C.

Source: Acta crystallographica.Section D.Structural biology. 78(11):1303-1314

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100163911312.0x000001&indx=1&recIds=ETOCvdc_100163911312.0x000001

AlphaFold and the future of structural biology

Authors: Read, Randy J., Baker, Edward N., Bond, Charles S., Garman, Elspeth F., van Raaij, Mark J.

Source: Acta crystallographica.Section F.Structural biology communications. 79(7):166-168

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100187209628.0x000001&indx=1&recIds=ETOCvdc_100187209628.0x000001

30 years of Acta D

Authors: Garman, Elspeth F., Read, Randy J., Bond, Charles S.

Source: Acta crystallographica.Section D.Structural biology. 79(2):95-97

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100173623480.0x000001&indx=1&recIds=ETOCvdc_100173623480.0x000001

Assessing the utility of CASP14 models for molecular replacement

Authors: Millán, Claudia, Keegan, Ronan M., Pereira, Joana, Sammito, Massimo D., Simpkin, Adam J., McCoy, Airlie J., Lupas, Andrei N., Hartmann, Marcus D., Rigden, Daniel J., Read, Randy J.

Source: Proteins. 89(12):1752-1769

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100134836081.0x000001&indx=1&recIds=ETOCvdc_100134836081.0x000001

Likelihood‐based estimation of substructure content from single‐wavelength anomalous diffraction (SAD) intensity data

Authors: Hatti, Kaushik S., McCoy, Airlie J., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 77(7):880-893

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100122571243.0x000001&indx=1&recIds=ETOCvdc_100122571243.0x000001

Adaptive Cartesian and torsional restraints for interactive model rebuilding

Authors: Croll, Tristan Ian, Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 77(4):438-446

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100121108672.0x000001&indx=1&recIds=ETOCvdc_100121108672.0x000001

Detection of translational noncrystallographic symmetry in Patterson functions

Authors: Caballero, Iracema, Sammito, Massimo D., Afonine, Pavel V., Usón, Isabel, Read, Randy J., McCoy, Airlie J.

Source: Acta crystallographica.Section D.Structural biology. 77(2):131-141

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100114552517.0x000001&indx=1&recIds=ETOCvdc_100114552517.0x000001

Phasertng: directed acyclic graphs for crystallographic phasing

Authors: McCoy, Airlie J., Stockwell, Duncan H., Sammito, Massimo D., Oeffner, Robert D., Hatti, Kaushik S., Croll, Tristan I., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 77(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100114295254.0x000001&indx=1&recIds=ETOCvdc_100114295254.0x000001

Multimeric structure of a subfamily III haloalkane dehalogenase‐like enzyme solved by combination of cryo‐EM and x‐ray crystallography

Authors: Chmelova, Klaudia, Gao, Tadeja, Polak, Martin, Schenkmayerova, Andrea, Croll, Tristan I., Shaikh, Tanvir R., Skarupova, Jana, Chaloupkova, Radka, Diederichs, Kay, Read, Randy J., Damborsky, Jiri, Novacek, Jiri, Marek, Martin

Source: Protein science. 32(10)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195918030.0x000001&indx=1&recIds=ETOCvdc_100195918030.0x000001

Germline mutations in the transcription factor IKZF5 cause thrombocytopenia

Authors: Lentaigne, Claire ^{1, 2, 3, *}, Greene, Daniel ^{3, 4, 5, *}, Sivapalaratnam, Suthesh ^{3, 6, *}, Favier, Remi ^{7, 8, *}, Seyres, Denis ^{3, 4, 9}, Thys, Chantal ¹⁰, Grassi, Luigi ^{3, 4, 9}, Mangles, Sarah ¹¹, Sibson, Keith ¹², Stubbs, Matthew ¹, Burden, Frances ^{3, 4, 9}, Bordet, Jean-Claude ¹³, Armari-Alla, Corinne ¹⁴, Erber, Wendy ^{3, 15, 16}, Farrow, Samantha ^{3, 4, 9}, Gleadall, Nicholas ^{3, 4}, Gomez, Keith ¹⁷, Megy, Karyn ^{3, 4, 9}, Papadia, Sofia ^{3, 4, 9}, Penkett, Christopher J. ^{3, 4, 9}, Sims, Matthew C. ³, Stefanucci, Luca ^{3, 4}, Stephens, Jonathan C. ^{3, 4, 9}, Read, Randy J. ¹⁸, Stirrups, Kathleen E. ^{3, 4, 9}, Ouwehand, Willem H. ^{3, 4, 9, 19}, Laffan, Michael A. ^{1, 2}, Frontini, Mattia ^{3, 9, 20}, Freson, Kathleen ^{3, 10}, Turro, Ernest ^{3, 4, 5, 9}

Source: In Blood 5 December 2019 134(23):2070-2081

Density modification of cryo‐EM maps

Authors: Terwilliger, Thomas C., Sobolev, Oleg V., Afonine, Pavel V., Adams, Paul D., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 76(10):912-925

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100108164945.0x000001&indx=1&recIds=ETOCvdc_100108164945.0x000001

Measuring and using information gained by observing diffraction data

Authors: Read, Randy J., Oeffner, Robert D., McCoy, Airlie J.

Source: Acta crystallographica.Section D.Structural biology. 76(3):238-247

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100103608431.0x000001&indx=1&recIds=ETOCvdc_100103608431.0x000001

Factors influencing estimates of coordinate error for molecular replacement

Authors: Hatti, Kaushik S., McCoy, Airlie J., Oeffner, Robert D., Sammito, Massimo D., Read, Randy J.

Source: Acta crystallographica.Section D.Structural biology. 76(1):19-27

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100097856398.0x000001&indx=1&recIds=ETOCvdc_100097856398.0x000001

Likelihood‐based interactive local docking into cryo‐EM maps in ChimeraX.

Authors: Read, Randy J.¹ (AUTHOR) rjr27@cam.ac.uk, Pettersen, Eric F.² (AUTHOR), McCoy, Airlie J.¹ (AUTHOR), Croll, Tristan I.³ (AUTHOR), Terwilliger, Thomas C.⁴ (AUTHOR), Poon, Billy K.⁵ (AUTHOR), Meng, Elaine C.² (AUTHOR), Liebschner, Dorothee⁵ (AUTHOR), Adams, Paul D.^5,6 (AUTHOR)

Source: Acta Crystallographica: Section D, Structural Biology. Aug2024, Vol. 80 Issue 8, p588-598. 11p.

Subject Terms: *NOISE, *SPEED, *COMPUTER software, *HYPOTHESIS