Kathryn Cowtan

Search results

• 2024

  Automated Model Building with ModelCraft

  Bond, P., Dialpuri, J. & Cowtan, K. D., 21 Jul 2024.

  Research output: Contribution to conference › Poster

• NucleoFind: a deep-learning network for interpreting nucleic acid electron density

  Dialpuri, J. S., Agirre, J., Cowtan, K. D. & Bond, P. S., 20 Aug 2024, (E-pub ahead of print) In: Nucleic Acids Research. 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

  Lawson, C. L., Kryshtafovych, A., Pintilie, G. D., Burley, S. K., Černý, J., Chen, V. B., Emsley, P., Gobbi, A., Joachimiak, A., Noreng, S., Prisant, M. G., Read, R. J., Richardson, J. S., Rohou, A. L., Schneider, B., Sellers, B. D., Shao, C., Sourial, E., Williams, C. I. & Williams, C. J. & 61 others, Yang, Y., Abbaraju, V., Afonine, P. V., Baker, M. L., Bond, P. S., Blundell, T. L., Burnley, T., Campbell, A., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K. D., DiMaio, F., Esmaeeli, R., Giri, N., Grubmüller, H., Hoh, S. W., Hou, J., Hryc, C. F., Hunte, C., Igaev, M., Joseph, A. P., Kao, W. C., Kihara, D., Kumar, D., Lang, L., Lin, S., Maddhuri Venkata Subramaniya, S. R., Mittal, S., Mondal, A., Moriarty, N. W., Muenks, A., Murshudov, G. N., Nicholls, R. A., Olek, M., Palmer, C. M., Perez, A., Pohjolainen, E., Pothula, K. R., Rowley, C. N., Sarkar, D., Schäfer, L. U., Schlicksup, C. J., Schröder, G. F., Shekhar, M., Si, D., Singharoy, A., Sobolev, O. V., Terashi, G., Vaiana, A. C., Vedithi, S. C., Verburgt, J., Wang, X., Warshamanage, R., Winn, M. D., Weyand, S., Yamashita, K., Zhao, M., Schmid, M. F., Berman, H. M. & Chiu, W., 1 Jul 2024, In: Nature Methods. 21, 7, p. 1340-1348 9 p.

  Research output: Contribution to journal › Article › peer-review
• 2023

  Buccaneer model building with neural network fragment selection

  Alharbi, E., Calinescu, R. & Cowtan, K. D., 28 Mar 2023, In: Acta crystallographica. Section D, Structural biology. 79, 4, p. 326-338 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• The CCP4 suite: integrative software for macromolecular crystallography

  Agirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Baslé, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Mármol, J. J., Berrisford, J. M., Bond, P. S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A. G., Cowtan, K. D., Croll, T. I., Debreczeni, J. É., Devenish, N. E. & Dodson, E. J. & 74 others, Drevon, T. R., Emsley, P., Evans, G., Evans, P. R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E. F., Gerstel, M., Gildea, R. J., Hatti, K., Hekkelman, M. L., Heuser, P., Hoh, S. W., Hough, M. A., Jenkins, H. T., Jiménez, E., Joosten, R. P., Keegan, R. M., Keep, N., Krissinel, E. B., Kolenko, P., Kovalevskiy, O., Lamzin, V. S., Lawson, D. M., Lebedev, A. A., Leslie, A. G. W., Lohkamp, B., Long, F., Malý, M., McCoy, A. J., McNicholas, S. J., Medina, A., Millán, C., Murray, J. W., Murshudov, G. N., Nicholls, R. A., Noble, M. E. M., Oeffner, R., Pannu, N. S., Parkhurst, J. M., Pearce, N., Pereira, J., Perrakis, A., Powell, H. R., Read, R. J., Rigden, D. J., Rochira, W., Sammito, M., Sánchez Rodríguez, F., Sheldrick, G. M., Shelley, K. L., Simkovic, F., Simpkin, A. J., Skubak, P., Sobolev, E., Steiner, R. A., Stevenson, K., Tews, I., Thomas, J. M. H., Thorn, A., Valls, J. T., Uski, V., Usón, I., Vagin, A., Velankar, S., Vollmar, M., Walden, H., Waterman, D., Wilson, K. S., Winn, M. D., Winter, G., Wojdyr, M. & Yamashita, K., 1 Jun 2023, In: Acta crystallographica. Section D, Structural biology. 79, Pt 6, p. 449-461 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2022

  Atomic model validation using the CCP-EM software suite

  Joseph, A. P., Olek, M., Malhotra, S., Zhang, P., Cowtan, K., Burnley, T. & Winn, M. D., 1 Feb 2022, In: Acta Crystallographica Section D: Structural Biology. 78, p. 152-161 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• CCP4 Cloud for structure determination and project management in macromolecular crystallography

  Krissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O., Nicholls, R. A., Pannu, N. S., Skubák, P., Berrisford, J., Fando, M., Lohkamp, B., Wojdyr, M., Simpkin, A. J., Thomas, J. M. H., Oliver, C., Vonrhein, C., Chojnowski, G., Basle, A. & Purkiss, A. & 13 others, Isupov, M. N., McNicholas, S., Lowe, E., Triviño, J., Cowtan, K., Agirre, J., Rigden, D. J., Uson, I., Lamzin, V., Tews, I., Bricogne, G., Leslie, A. G. W. & Brown, D. G., 1 Sept 2022, In: Acta crystallographica. Section D, Structural biology. 78, Pt 9, p. 1079-1089 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice

  Olek, M. & Cowtan, K. D., 7 Apr 2022, In: Structure. 30, 4, p. 522-531

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• ModelCraft: an advanced automated model-building pipeline using Buccaneer

  Bond, P. S. & Cowtan, K. D., 1 Sept 2022, In: Acta crystallographica. Section D, Structural biology. 78, p. 1090-1098 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2021

  Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

  Lawson, C. L., Kryshtafovych, A., Adams, P. D., Afonine, P. V., Baker, M. L., Barad, B. A., Bond, P., Burnley, T., Cao, R., Cheng, J., Chojnowski, G., Cowtan, K., Dill, K. A., DiMaio, F., Farrell, D. P., Fraser, J. S., Herzik, M. A., Hoh, S. W., Hou, J. & Hung, L. W. & 34 others, Igaev, M., Joseph, A. P., Kihara, D., Kumar, D., Mittal, S., Monastyrskyy, B., Olek, M., Palmer, C. M., Patwardhan, A., Perez, A., Pfab, J., Pintilie, G. D., Richardson, J. S., Rosenthal, P. B., Sarkar, D., Schäfer, L. U., Schmid, M. F., Schröder, G. F., Shekhar, M., Si, D., Singharoy, A., Terashi, G., Terwilliger, T. C., Vaiana, A., Wang, L., Wang, Z., Wankowicz, S. A., Williams, C. J., Winn, M., Wu, T., Yu, X., Zhang, K., Berman, H. M. & Chiu, W., 4 Feb 2021, In: Nature Methods. 18, 2, p. 156-164 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• GloSAT homogenization: GitHub repository for software code

  Cowtan, K. D., 1 Jul 2021

  Research output: Non-textual form › Software

• Predicting the performance of automated crystallographic model-building pipelines

  Alharbi, E., Bond, P., Calinescu, R. & Cowtan, K., 1 Dec 2021, In: Acta crystallographica. Section D, Structural biology. 77, Pt 12, p. 1591-1601 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• 'Sheetbend' software for model morphing of atomic models. version 0.5

  Cowtan, K. D., 18 Apr 2021

  Research output: Non-textual form › Software

• 2020

  Comment on ''the impact of recent forcing and ocean heat uptake data on estimates of climate sensitivity''

  Cowtan, K. & Jacobs, P., 1 Jan 2020, In: Journal of Climate. 33, 1, p. 391-396 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM

  Hoh, S. W., Burnley, T. & Cowtan, K., 1 Jun 2020, In: Acta crystallographica. Section D, Structural biology. 76, Part 6, p. 531-541 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Pacific variability reconciles observed and modelled global mean temperature increase since 1950

  Stolpe, M. B., Cowtan, K., Medhaug, I. & Knutti, R., 28 Oct 2020, In: Climate Dynamics. 22 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Pairwise running of automated crystallographic model-building pipelines

  Alharbi, E., Calinescu, R. & Cowtan, K., 1 Sept 2020, In: Acta Crystallographica Section D: Structural Biology. 76, 9, p. 814-823 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Predicting protein model correctness in Coot using machine learning

  Bond, P. S., Wilson, K. S. & Cowtan, K. D., 1 Aug 2020, In: Acta crystallographica. Section D, Structural biology. 76, Pt 8, p. 713-723 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Shift-field refinement of macromolecular atomic models

  Cowtan, K. D., Metcalfe, S. A. & Bond, P., Dec 2020, In: Acta crystallographica. Section D, Structural biology. 76, 12, p. 1192-1200

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Structural barriers to scientific progress

  Cowtan, K. D., Oct 2020, In: Acta Crystallographica Section D: Structural Biology. 76, 10, p. 908-911 4 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2019

  A limited role for unforced internal variability in 20th century warming.

  Cowtan, K. D., 16 May 2019, (E-pub ahead of print) In: Journal of Climate.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Comparison of automated crystallographic model-building pipelines

  Alharbi, E., Bond, P. S., Calinescu, R. & Cowtan, K., 1 Dec 2019, In: Acta crystallographica. Section D, Structural biology. 75, Pt 12, p. 1119-1128 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Erratum: The 'pause' in global warming in historical context: II. Comparing models to observations (Environmental Research Letters (2018)13 (123007) DOI: 10.1088/1748-9326/aaf372)

  Lewandowsky, S., Cowtan, K., Risbey, J. S., Mann, M. E., Steinman, B. A., Oreskes, N. & Rahmstorf, S., 26 Mar 2019, In: Environmental Research Letters. 14, 4, 049601.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

• 'Sheetbend' software for model morphing of atomic models. version 0.2

  Cowtan, K. D., 12 Nov 2019

  Research output: Non-textual form › Software

• 2018

  A fluctuation in surface temperature in historical context: Reassessment and retrospective on the evidence

  Risbey, J. S., Lewandowsky, S., Cowtan, K., Oreskes, N., Rahmstorf, S., Jokimäki, A. & Foster, G., 19 Dec 2018, In: Environmental Research Letters. 13, 12, 23 p., 123008.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• CCP4i2: The new graphical user interface to the CCP4 program suite

  Potterton, L., Agirre, J., Ballard, C. C., Cowtan, K., Dodson, E., Evans, P. R., Jenkins, H. T., Keegan, R., Krissinel, E. B., Stevenson, K., Lebedev, A., Mcnicholas, S. J., Nicholls, R. A., Noble, M., Pannu, N. S., Roth, C., Sheldrick, G. M., Skubak, P., Turkenburg, J. & Uski, V. & 5 others, von Delft, F., Waterman, D. G., Wilson, K., Winn, M. & Wojdyr, M., 1 Feb 2018, In: Acta crystallographica. Section D, Structural biology. 74, 2, p. 68-84 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• CCP-EM stable release versions 1.0.0 to 1.6

  Cowtan, K. D. (Developer) & Hoh, S. W. (Developer), 9 Apr 2018

  Research output: Non-textual form › Software

• Evaluating biases in sea surface temperature records using coastal weather stations

  Cowtan, K. D., Rohde, R. & Hausfather, Z., 29 Aug 2018, In: Quarterly Journal of the Royal Meteorological Society. 144, 712, p. 670-681 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Global temperature definition affects achievement of long-term climate goals

  Richardson, M., Cowtan, K. & Millar, R. J., 1 May 2018, In: Environmental Research Letters. 13, 5, p. 1-8 8 p., 054004.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Macromolecular refinement by model morphing using non-atomic parameterizations

  Cowtan, K. & Agirre, J., 7 Mar 2018, In: Acta crystallographica. Section D, Structural biology.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Reply to: Interpretations of the Paris climate target

  Schurer, A. P., Cowtan, K., Hawkins, E., Mann, M. E., Scott, V. & Tett, S. F. B., 19 Mar 2018, (E-pub ahead of print) In: Nature Geoscience. 11, p. 220-21 2 p.

  Research output: Contribution to journal › Letter › peer-review

• 'Sheetbend' software for model morphing of atomic models. version 0.1

  Cowtan, K. D., 19 Jul 2018

  Research output: Non-textual form › Software

• Statistical analysis of coverage error in simple global temperature estimators

  Cowtan, K. D., Jacobs, P., Thorne, P. & Wilkinson, R., 20 Jul 2018, (E-pub ahead of print) In: Dynamics and Statistics of the Climate System: An Interdisciplinary Journal. 28 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• The 'pause' in global warming in historical context: (II). Comparing models to observations

  Lewandowsky, S., Cowtan, K., Risbey, J. S., Mann, M. E., Steinman, B. A., Oreskes, N. & Rahmstorf, S., 19 Dec 2018, In: Environmental Research Letters. 13, 12, 26 p., 123007.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2017

  Assessing recent warming using instrumentally homogeneous sea surface temperature records

  Hausfather, Z., Cowtan, K., Clarke, D. C., Jacobs, P., Richardson, M. & Rohde, R., 4 Jan 2017, In: Science Advances. 3, 1, p. 1-13 13 p., e1601207.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Automating tasks in protein structure determination with the Clipper Python module

  McNicholas, S., Croll, T., Burnley, T., Palmer, C. M., Hoh, S. W., Jenkins, H. T., Dodson, E., Cowtan, K. & Agirre, J., 13 Sept 2017, In: Protein science : a publication of the Protein Society. p. 1-24 24 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Carbohydrate structure: the rocky road to automation

  Agirre, J., Davies, G. J., Wilson, K. S. & Cowtan, K. D., 2017, In: CURRENT OPINION IN STRUCTURAL BIOLOGY. 44, p. 39-47 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Stay Out of Scientists' E-mails

  Cowtan, K. & Hausfather, Z., 14 Mar 2017, In: Scientific american. 316, 4, p. 12 1 p.

  Research output: Contribution to journal › Comment/debate
• 2016

  Evaluating the impact of U.S. Historical Climatology Network homogenization using the U.S. Climate Reference Network

  Hausfather, Z., Cowtan, K., Menne, M. J. & Williams, C. N., 25 Feb 2016, In: Geophysical Research Letters. 43, 4, p. 1695-1701

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Reconciled climate response estimates from climate models and the energy budget of Earth

  Richardson, M., Cowtan, K., Hawkins, E. & Stolpe, M. B., Oct 2016, In: Nature Climate Change. 6, 10, p. 931-935 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases

  Agirre, J., Ariza, A., Offen, W. A., Turkenburg, J. P., Roberts, S. M., McNicholas, S., Harris, P. V., McBrayer, B., Dohnalek, J., Cowtan, K. D., Davies, G. J. & Wilson, K. S., 1 Feb 2016, In: Acta crystallographica. Section D, Structural biology. 72, 2, p. 254-265 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
• 2015

  Carbohydrate anomalies in the PDB

  Agirre, J., Davies, G., Wilson, K. & Cowtan, K., 2015, In: NATURE CHEMICAL BIOLOGY. 11, 5, p. 303 1 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access

  File

• Corrigendum to "On a minimal model for estimating climate sensitivity" [Ecol. Model. 297 (2015) 20-25]

  Cawley, G. C., Cowtan, K., Way, R. G., Jacobs, P. & Jokimäki, A., 24 Sept 2015, In: Ecological Modelling. 312, p. 102-103 2 p.

  Research output: Contribution to journal › Article

• On a minimal model for estimating climate sensitivity

  Cawley, G. C., Cowtan, K., Way, R. G., Jacobs, P. & Jokimäki, A., 10 Feb 2015, In: Ecological Modelling. 297, p. 20-25 6 p.

  Research output: Contribution to journal › Article › peer-review

• Privateer: software for the conformational validation of carbohydrate structures

  Agirre, J., Iglesias-Fernández, J., Rovira, C., Davies, G. J., Wilson, K. S. & Cowtan, K. D., 4 Nov 2015, In: Nature Structural & Molecular Biology. 22, 11, p. 833-834 2 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access

  File

• Reply to Comment on 'Quantifying the consensus on anthropogenic global warming in the scientific literature'

  Cook, J. & Cowtan, K. D., Mar 2015, In: Environmental Research Letters. 10, 3, 039002.

  Research output: Contribution to journal › Comment/debate › peer-review

• Robust comparison of climate models with observations using blended land air and ocean sea surface temperatures

  Cowtan, K., Hausfather, Z., Hawkins, E., Jacobs, P., Mann, M. E., Miller, S. K., Steinman, B. A., Stolpe, M. B. & Way, R. G., 26 Aug 2015, In: Geophysical Research Letters. 42, 15, p. 6526-6534 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Validation of carbohydrate structures in CCP4 6.5

  Agirre, J. & Cowtan, K. D., 2015, 3 p.

  Research output: Other contribution

  Open Access

  File
• 2014

  Automated nucleic acid chain tracing in real time

  Cowtan, K., Nov 2014, In: IUCrJ. 1, 6, p. 387-392 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

• Buccaneer version 1.6.0

  Cowtan, K. D., 7 May 2014

  Research output: Non-textual form › Software