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JSB Special Issue: Coming Soon

More than half of the articles that will appear in the Journal of Structural Biology Special Issue on the 2016 CryoEM Map and Model Challenges are already accepted for publication and are either already online or will shortly appear there, as listed below.  Click here for access.

Map Challenge

  • Heymann, B. (2018). "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."
  • Stagg, S. M. and Mendez, J. H. (2018). "Processing Apoferritin with the Appion Pipeline."

Map Challenge Assessment

  • Heymann, B. (2018). "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."
  • Terashi, G. and Kihara, D. (2018). "De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge."
  • Pintilie, G. and Chiu, W. (2018). "Assessment of Structural Features in Cryo-EM Density Maps using SSE and Side Chain Z-Scores."
  • 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

  • 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."

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."

 

EMDataBank Validation Challenges are supported by NIH National Institute of General Medical Sciences

Please send your challenge questions, comments and feedback to challenges@emdatabank.org

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