WikiSysop: Created page with "== Citation == Mondal, D., Kumar, V., Satler, T., Ramachandran, R., Saltzberg, D., Chemmama, I., Pilla, K.B., Echeverria, I., Webb, B.M., Gupta, M. and others 2025. Recognizing amino acid sidechains in a medium-resolution cryo-electron density map. Protein Science. 34, 8 (2025), e70217. == Abstract == Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 Å resolution is difficult. To facilitate this t..."

2026-02-12T08:59:24Z

Created page with "== Citation == Mondal, D., Kumar, V., Satler, T., Ramachandran, R., Saltzberg, D., Chemmama, I., Pilla, K.B., Echeverria, I., Webb, B.M., Gupta, M. and others 2025. Recognizing amino acid sidechains in a medium-resolution cryo-electron density map. Protein Science. 34, 8 (2025), e70217. == Abstract == Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 Å resolution is difficult. To facilitate this t..."

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== Citation ==

Mondal, D., Kumar, V., Satler, T., Ramachandran, R., Saltzberg, D., Chemmama, I., Pilla, K.B., Echeverria, I., Webb, B.M., Gupta, M. and others 2025. Recognizing amino acid sidechains in a medium-resolution cryo-electron density map. Protein Science. 34, 8 (2025), e70217.

== Abstract ==

Building an accurate atomic structure model of a protein into a cryo-electron microscopy (cryo-EM) map at worse than 3 Å resolution is difficult. To facilitate this task, we devised a method for assigning the amino acid residue sequence to the backbone fragments traced in an input cryo-EM map (EMSequenceFinder). EMSequenceFinder relies on a Bayesian scoring function for ranking 20 standard amino acid residue types at a given backbone position, based on the fit to a density map, map resolution, and secondary structure propensity. The fit to a density is quantified by a convolutional neural network that was trained on ~5.56 million amino acid residue densities extracted from cryo-EM maps at 3–10 Å resolution and corresponding atomic structure models deposited in the Electron Microscopy Data Bank (EMDB). We benchmarked EMSequenceFinder by predicting the sequences of 58,044 distinct ɑ-helix and β-strand fragments, given the fragment backbone coordinates fitted in their density maps. EMSequenceFinder identifies the correct sequence as the best-scoring sequence in 77.8% of these cases. We also assessed EMSequenceFinder on separate datasets of cryo-EM maps at resolutions from 4 to 6 Å. The accuracy of EMSequenceFinder (58%) was better than that of three tested state-of-the-art methods, including findMysequence (45%), ModelAngelo (27%), and sequence_from_map in Phenix (12.9%). We further illustrate EMSequenceFinder by threading the Severe Acute Respiratory Syndrome Coronavirus 2 Non-Structural Protein 2 sequence into eight cryo-EM maps at resolutions from 3.7 to 7.0 Å. EMSequenceFinder is implemented in our open-source Integrative Modeling Platform (IMP) program. Thus, it is expected to be helpful for integrative structure modeling based on a cryo-EM map and other information, such as models of protein complex components and chemical crosslinks between them. EMSequenceFinder is available as part of our open-source IMP distribution at https://integrativemodeling.org/.

== Keywords ==

== Links ==

https://onlinelibrary.wiley.com/doi/full/10.1002/pro.70217

== Related software ==

== Related methods ==

== Comments ==

2025Mondal EMSequenceFinder - Revision history