published Thu, 08/09/2018 - 15:41
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