JSB Special Issue

Articles published in the Journal of Structural Biology Special Issue on the CryoEM Map and Model Challenges are listed below.  Many thanks to all who have contributed!

Special Issue Title: The CryoEM Structure Map and Model Challenges

Editorial

• Lawson, C.L. and Chiu, W. (2018). "Comparing Cryo-EM Structures"

Map Challenge

• Stagg, S. M. and Mendez, J. H. (2018). "Processing Apoferritin with the Appion Pipeline."
• Heymann, B. (2018a). "Single Particle Reconstruction and Validation using Bsoft for the Map Challenge."
• Sorzano, C. O. S., Vargas, J., Trevin, J. M. R., Jiménez, A., Melero, R., Martinez, M., Ramírez-Aportela, E., Conesa, P., Vilas, J. L., Marabini, R. and Carazo, J. M. (2018). "A new algorithm for high-resolution reconstruction of Single Particles by Electron Microscopy."
• Bell, J. M., Fluty, A. C., Durmaz, T., Chen, M. and Ludtke, S. J. (2018). "New software tools in EMAN2 inspired by EMDatabank map challenge."
• Donati, L., Nilchian, M., Sorzano, C. O. S. and Unser, M. (2018). "Fast Multiresolution Reconstruction for Cryo-EM."

Map Challenge Assessment

• Heymann, B. (2018b). "Map Challenge Assessment: Fair comparison of single particle cryoEM reconstructions."
• Jonic, S. (2018). "A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps."
• Pintilie, G. and Chiu, W. (2018). "Assessment of Structural Features in Cryo-EM Density Maps using SSE and Side Chain Z-Scores."
• Marabini, R., Kazemi, M., Sorzano, C. O. S. and Carazo, J.-M. (2018). "Map Challenge: Analysis using Pair Comparison Method."
• Stagg, S. M. and Mendez, J. H. (2018). "Assessing the quality of single particle reconstructions by atomic model building."
• Heymann, B., Marabini, R., Kazemi, M., Sorzano, C.O.S., Holmdahl, M., Mendez, J.H., Stagg, S.M., Jonic, S., Palovcak, E., Armache, J.-P., Zhao, J., Cheng, Y., Pintilie, G., Chiu, W., Patwardhan, A., and Carazo, J.-M. (2018). "The First Single Particle Analysis Map Challenge: A Summary of the Assessments."

Model Challenge

• Terashi, G. and Kihara, D. (2018). "De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge."
• Terwilliger, T., Adams, P. D., Afonine, P. V. and Sobolev, O. V. (2018). "Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge."
• Wang, Y., Shekhar, M., Thifault, D., Williams, C. J., McGreevey, R., Richardson, J. S., Singharoy, A. and Tajkhorshid, E. (2018). "Constructing Atomic Structural Models into Cryo-EM densities using Molecular Dynamics - Pros and Cons."
• Yu, I., Nguyen, L., Avaylon, J., Wang, K. and Zhou, Z. H. (2018). "Building Atomic Models Based on Near Atomic Resolution cryoEM Maps with Existing Tools."
• Chen, M. and Baker, M. L. (2018). "Automation And Assessment Of De Novo Modeling With Pathwalking In Near Atomic Resolution CryoEM Density Maps."

Model Challenge Assessment

• Kryshtafovych, A., Adams, P. D., Lawson, C. L. and Chiu, W. (2018). "Evaluation System and Web Infrastructure for the Second Cryo-EM Model Challenge."
• Richardson, J. S., Williams, C. J., Videau, L. L. and Chen, V. B. (2018). "Assessment of detailed conformations suggests strategies for improving cryoEM models: helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale."

Related Datasets

• Kryshtafovych, A., Adams, P.D., Lawson, C.L., Chiu, W., 2018. Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge, Data in Brief.
• Lawson, C.L., Chiu, W., Carragher, B., Carazo, J.-M., Jiang, W., Patwardhan, A., Rubinstein, J., Rosenthal, P., Sun, F., Vonck, J., Bai, X., Bell, J., Caputo, N., Chakraborty, A., Chen, D.-H., Chen, J., Diaz-Avalos, R., Donati, L., Estrozi, L., Galaz Montoya, J., Gati, C., Gomez-Blanco, J., Grigorieff, N., Gros, P., Heymann, B., Leith, A., Li, F., Ludtke, S., Nans, A., Nilchian, M., Punjabi, A., Sixma, T., Tegunov, D., Yang, K., Yu, G., Zhang, J., Sala, R., 2017. CryoEM Maps and Associated Data Submitted to the 2015/2016 EMDataBank Map Challenge. version 1.1, Zenodo.
• Lawson, C.L., Kryshtafovych, A., Chiu, W., Adams, P., Brünger, A., Kleywegt, G., Patwardhan, A., Read, R., Schwede, T., Topf, M., Afonine, P., Avaylon, J., Baker, M., Braun, T., Cao, W., Chittori, S., Croll, T., DiMaio, F., Frenz, B., Grudinin, S., Hoffmann, A., Hryc, C., Joseph, A.P., Kawabata, T., Kihara, D., Mao, B., Matthies, D., McGreevy, R., Nakamura, H., Nakamura, S., Nguyen, L., Schroeder, G., Shekhar, M., Shimizu, K., Singharoy, A., Sobolev, O., Tajkhorshid, E., Teo, I., Terashi, G., Terwilliger, T., Wang, K., Yu, I., Zhou, H., Sala, R., 2018. CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge. version 1.1, Zenodo.

Last update: 2020-04-14