ISOLDE: Bringing structural biology to life

Publications

Citing ISOLDE

If you use ISOLDE in work leading to a publication, please read and cite the following paper:

Croll, Tristan Ian. 2018. “ISOLDE: A Physically Realistic Environment for Model Building into Low-Resolution Electron-Density Maps.” Acta Crystallographica Section D: Structural Biology 74 (6):519–30. doi: 10.1107/S2059798318002425.

Publications related to ISOLDE or IMDFF

2021

Croll, Tristan I and Read, R. 2021. "Adaptive Cartesian and torsional restraints for interactive model rebuilding." Acta Crystallographica Section D: Biological Crystallography. In press.

Thomson, Emma C, Laura E Rosen, James G Shepherd, Roberto Spreafico, Ana da Silva Filipe, Jason A Wojcechowskyj, Chris Davis, Luca Piccoli, David J Pascall, Josh Dillen, Spyros Lytras, Nadine Czudnochowski, Rajiv Shah, Marcel Meury, Natasha Jesudason, Anna De Marco, Kathy Li, Jessica Bassi, Aine O’Toole, Dora Pinto, Rachel M Colquhoun, Katja Culap, Ben Jackson, Fabrizia Zatta, Andrew Rambaut, Stefano Jaconi, Vattipally B Sreenu, Jay Nix, Ivy Zhang, Ruth F Jarrett, William G Glass, Martina Beltramello, Kyriaki Nomikou, Matteo Pizzuto, Lily Tong, Elisabetta Cameroni, Tristan I Croll, Natasha Johnson, Julia Di Iulio, Arthur Wickenhagen, Alessandro Ceschi, Aoife M Harbison, Daniel Mair, Paolo Ferrari, Katherine Smollett, Federica Sallusto, Stephen Carmichael, Christian Garzoni, Jenna Nichols, Massimo Galli, Joseph Hughes, Agostino Riva, Antonia Ho, Marco Schiuma, Malcolm G Semple, Peter JM Openshaw, Elisa Fadda, J Kenneth Baillie, John D Chodera, Suzannah J Rihn, Samantha J Lycett, Herbert W Virgin, Amalio Telenti, Davide Corti, David L Robertson, Gyorgy Snell, and ISARIC4C Investigators. 2021. "Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity." Cell 184(5): 1171-1187.e20. doi: 10.1016/j.cell.2021.01.037

Pettersen, Eric F, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I croll, John H Morris, and Thomas E Ferrin. 2021. "UCSF ChimeraX: Structure visualization for researchers, educators, and developers." Protein Science 30(1): 70-82. doi: 10.1002/pro.3943

Croll, Tristan I, Christopher J Williams, Vincent B Chen, David C Richardson, and Jane S Richardson. 2021. "Improving SARS-CoV-2 structures: peer review by early coordinate release." Biophysical Journal online ahead of print. doi: 10.1016/j.bpj.2020.12.029

2020

Retana, Tania R., Jack Bradley-Clarke, Tristan Croll, Ruth Rose, Inva Hoti, Andrew J Stagg, Mayte Villalba, and Richard W. Pickersgill. 2020. "Lig v 1 structure and the inflammatory response to the Ole e 1 protein family." Allergy 75(9): 2395-2398. doi: 10.1111/all.14351

Lonhienne, Thierry, Yu Shang Low, Mario D. Garcia, Tristan Croll, Yan Gao, Quan Wang, Lou Brillault, Craig M. Williams, James A. Fraser, Ross P. McGeary, Nicholas P. West, Michael J. Landsberg, Zihe Rao, Gerhard Schenk, and Luke W. Guddat. 2020. "Structures of fungal and plant acetohydroxyacid synthases." Nature 586(7828): 317-321. doi: 10.1038/s41586-020-2514-3

Xu, Yibin, Nicholas S. Kirk, Hariprasad Venugopal, Mai B. Margetts, Tristan I. Croll, Jarrod J. Sandow, Andrew I. Webb, Carlie A. Delaine, Briony E. Forbes, and Michael C. Lawrence. 2020. "How IGF-II binds to the human type 1 insulin-like growth factor receptor." Structure 28(7): 786-798.e6. doi: 10.1016/j.str.2020.05.002

Woo, Hyeonuk, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, Jumin Lee, Min Sun Yeom, Tristan I. Croll, Chaok Seok, and Wonpil Im. 2020. "Developing a fully-glycosylated full-length SARS-CoV-2 spike protein model in a viral membrane." Journal of Physical Chemistry B 124(33): 7128-7137. doi: 0.1021/acs.jpcb.0c04553

Rougé, Lionel, Nancy Chiang, Micah Steffek, Christine Kugel, Tristan I. Croll, Christine Tam, Alberto Estevez, Christopher P. Arthur, Christopher M. Koth, Claudio Ciferri, Edward Kraft, Jian Payandeh, Gerald Nakamura, James T. Koerber2, and Alexis Rohou. 2020. "Structure of CD20 in complex with the therapeutic monoclonal antibody rituximab." Science 367(6483): 1224-1230. doi:  10.1126/science.aaz9356

2019

Liebschner, Dorothee, Pavel V Afonine, Matthew L Baker, Gabor Bunkoczi, Vincent B Chen, Tristan Croll, Bradley Hintze, Li-Wei Hung, Swati Jain, Airlie McCoy, Nigel W Moriarty, Robert D Oeffner, Billy K Poon, Michael G Prisant, Randy Read, Jane S Richardson, David C Richardson, Massimo Sammito, Oleg V Sobolev, Duncan H Stockwell, Thomas C Terwilliger, Alexandre G Urzhumtsev, Lizbeth L Videau, Christopher J Williams, and Paul D Adams. 2019. "Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix." Acta Crystallographica D75: 861-877. doi: 10.1107/S2059798319011471

Piper, Sarah J., Lou Brillault, Rosalba Rothnagel, Tristan I Croll, Joseph K Box, Irene Chassagnon, Sebastian Scherer, Kenneth N Goldie, Sandra A Jones, Femke Schepers, Lauren Hartley-Tassell, Thomas Ve, Jason N Busby, Julie E Dalziel, J Shaun Lott, Ben Hankamer, Henning Stahlberg, Mark RH Hurst, and Michael J Landsberg. 2019. "Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin." Nature Communications 10 (1): 1952. doi: 10.1038/s41467-019-09890-8

Gao, Chen, Mitchell A Pallett, Tristan I Croll, Geoffrey L Smith, and Stephen C Graham. 2019. "Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55." Journal of Biological Chemistry 294 (16): 6416-6429 doi: 10.1074/jbc.RA118.006561

2018

Croll, Tristan Ian. 2018. “ISOLDE: A Physically Realistic Environment for Model Building into Low-Resolution Electron-Density Maps.” Acta Crystallographica Section D: Structural Biology 74 (6):519–30. doi: 10.1107/S2059798318002425.

McNicholas, Stuart, Tristan Croll, Tom Burnley, Colin M. Palmer, Soon Wen Hoh, Huw T. Jenkins, Eleanor Dodson, Kevin Cowtan, and Jon Agirre. 2018. “Automating Tasks in Protein Structure Determination with the Clipper Python Module.” Protein Science 27 (1):207–16. doi: 10.1002/pro.3299.

Keough, Dianne T., Dominik Rejman, Radek Pohl, Eva Zborníková, Dana Hocková, Tristan Croll, Michael D Edstein, Geoff W Birrell, Marina Chavchich, Lieve MJ Naesens, Gregory K Pierens, Ian M Brereton, and Luke W Guddat. 2018. “Design of Plasmodium Vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors as Potential Antimalarial Therapeutics.” ACS Chemical Biology 13 (1):82–90. doi: acschembio.7b00916.

2017

Ve, Thomas, Parimala R Vajjhala, Andrew Hedger, Tristan Croll, Frank DiMaio, Shane Horsefield, Xiong Yu, Peter Lavrencic, Zahid Hassan, Garry P Morgan, Ashley Mansell, Mehdi Mobli, Ailis O'Carroll, Brieuc Chauvin, Yann Gambin, Emma Sierecki, Michael J Landsberg, Katryn J Stacey, Edward H Egelman, and Bostjan Kobe. 2017. “Structural Basis of TIR-Domain-Assembly Formation in MAL- and MyD88-Dependent TLR4 Signaling.” Nature Structural & Molecular Biology 24 (9). doi: 10.1038/nsmb.3444.

Focht, Dorota, Tristan I. Croll, Bjorn P. Pedersen, and Poul Nissen. 2017. “Improved Model of Proton Pump Crystal Structure Obtained by Interactive Molecular Dynamics Flexible Fitting Expands the Mechanistic Model for Proton Translocation in P-Type ATPases.” Frontiers in Physiology 8 (APR):202. doi: 10.3389/fphys.2017.00202.

Zhang, Xiaoxiao, Maud Bernoux, Adam R. Bentham, Toby E. Newman, Thomas Ve, Lachlan W. Casey, Tom M. Raaymakers, Jian Hu, Tristan I. Croll et al. 2017. “Multiple Functional Self-Association Interfaces in Plant TIR Domains.” Proceedings of the National Academy of Sciences 114 (10):E2046–52. doi: 10.1073/pnas.1621248114.

2016

Casey, Lachlan W, Peter Lavrencic, Adam R Bentham, Stella Cesari, Daniel J Ericsson, Tristan Croll, Dušan Turk, Peter A Anderson, Alan E Mark, Peter N Dodds, Mehdi Mobli, Bostjan Kobe, and Simon J Williams. 2016. “The CC Domain Structure from the Wheat Stem Rust Resistance Protein Sr33 Challenges Paradigms for Dimerization in Plant NLR Proteins.” Proceedings of the National Academy of Sciences 113 (45):12856–61. doi: 10.1073/pnas.1609922113.

Croll, Tristan Ian, and Gregers Rom Andersen. 2016. “Re-Evaluation of Low-Resolution Crystal Structures via Interactive Molecular-Dynamics Flexible Fitting (IMDFF): A Case Study in Complement C4.” Acta Crystallographica Section D: Structural Biology 72 (9):1006–16. doi: 10.1107/S2059798316012201.

Croll, Tristan I., Brian J. Smith, Mai B. Margetts, Jonathan Whittaker, Michael A. Weiss, Colin W. Ward, and Michael C. Lawrence. 2016. “Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain.” Structure 24 (3):469–76. doi: 10.1016/j.str.2015.12.014.

2015

Croll, Tristan Ian. 2015. “The Rate of Cis-Trans Conformation Errors Is Increasing in Low-Resolution Crystal Structures.” Acta Crystallographica Section D: Biological Crystallography 71 (3):706–9. 10.1107/S1399004715000826.

Presentations and Workshops

2018

(workshop) Croll, T. ISOLDE. Chimera and Cytoscape/STRING Course, Copenhagen, Denmark. 12 - 13 Nov, 2018

(presentation) Croll, T. ISOLDE: Macromolecular model building comes alive. PHENIX developers' meeting, Berkeley, USA. Sep, 2018

(poster) Croll, T., A. J. McCoy and R. Read. ISOLDE: Bringing macromolecular model building to life. 31st European Crystallography Meeting, Oviedo, Spain. 22 - 27 Aug, 2018

(workshop) Croll, T. ISOLDE. Instruct Course on Model Building and Refinement for High Resolution EM Maps (4th Icknield Workshop), Diamond Light Source, Didcot, UK. 1 - 4 May, 2018

(presentation) Croll, T. ISOLDE: Macromolecular model building comes alive. PHENIX developers' meeting, Santa Fe, USA. 26-29 Mar, 2016

2017

(presentation) Croll, T. ISOLDE: Interactive model building in a physically realistic environment. Conference on methods and applications in the frontier between MX and CryoEM, Barcelona, Spain. 19 - 21 Sep, 2017

(presentation) Croll, T. ISOLDE: A next-generation environment for interactive model building in low-resolution maps. CCP-EM/CCP-BIOSIM workshop, Leeds, UK. 14 Jul, 2017

(workshop) Croll, T. Low resolution refinement. Erice School of Crystallography, Erice, Italy. 2 - 11 Jun, 2017

(presentation) Croll, T. ISOLDE: A next-generation environment for interactive model building in low-resolution maps. CCP-EM Spring Symposium, Diamond Light Source, Didcot, UK. 24 - 26 Apr, 2017

2016

(presentation) Croll, T. Interactive molecular dynamics flexible fitting: a physically realistic environment for rapid and high-fidelity model building. 30th biennial meeting of the Society of Crystallographers of Australia and New Zealand, Hobart, Australia. 29 Mar - 1 Apr, 2016

(presentation) Croll, T. Interactive molecular dynamics flexible fitting: adding a sense of touch to structural biology. Talks and demonstrations given at Aarhus University, Cambridge MRC Laboratory of Molecular Biology, Diamond Light Source and Oxford Structural Genomics Consortium, Jan 2016

Structures produced using ISOLDE

PDB IDs: 6o1k, 6o1l, 6o1m (pictured: 6o1m)

Reference: Pei, X. Y., T. Dendooven, E. Sonnleitner, S. Chen, U. Bläsi, and B. F. Luisi . "Architectural principles for Hfq/Crc-mediated regulation of gene expression." Elife. 2019; 8:e43158. doi: 10.7554/eLife.43158

PDB ID: 6ogd

Reference: Piper, Sarah J., Lou Brillault, Rosalba Rothnagel, Tristan I Croll, Joseph K Box, Irene Chassagnon, Sebastian Scherer, Kenneth N Goldie, Sandra A Jones, Femke Schepers, Lauren Hartley-Tassell, Thomas Ve, Jason N Busby, Julie E Dalziel, J Shaun Lott, Ben Hankamer, Henning Stahlberg, Mark RH Hurst, and Michael J Landsberg. 2019. "Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin." Nature Communications 10 (1): 1952. doi: 10.1038/s41467-019-09890-8

PDB ID: 6i2m

Reference: Gao, C., M.A. Pallett, T.I. Croll, G.L. Smith and S.C. Graham, 2019. Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55. J. Biological Chemistry, in press. DOI:

PDB ID: 6g63

Reference: Bandyra, K.J., J.M Wandzik and B.F. Luisi, 2018. Substrate recognition and autoinhibition in the central ribonuclease RNase E. Mol. Cell. 72(2): 275-285.e4. DOI: 10.1016/j.molcel.2018.08.039

PDB ID: 6eyc

Reference: Croll, T.I. 2018, ISOLDE: a physically realistic environment for model building into low-resolution electron density maps. Acta Crystallographica D74: 519-530. DOI: 10.1107/S2059798318002425

ISOLDE is developed and maintained by Tristan Croll in the lab of Randy Read at the Cambridge Institute for Medical Research and supported by Prof. Read's Wellcome Trust Principal Research Fellowship 209407/Z/17/Z. Development and testing has been aided by the generous donation of a GTX Titan Xp GPU by NVIDIA Corporation.

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