{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/sequence-guided-protein-structure","title":"Sequence-guided protein structure determination using graph convolutional and recurrent networks","arxiv_id":"2007.06847","date":"2020-07-14","proceeding":null,"authors":["Po-Nan Li","Saulo H. P. de Oliveira","Soichi Wakatsuki","Henry van den Bedem"],"abstract":"Single particle, cryogenic electron microscopy (cryo-EM) experiments now routinely produce high-resolution data for large proteins and their complexes. Building an atomic model into a cryo-EM density map is challenging, particularly when no structure for the target protein is known a priori. Existing protocols for this type of task often rely on significant human intervention and can take hours to many days to produce an output. Here, we present a fully automated, template-free model building approach that is based entirely on neural networks. We use a graph convolutional network (GCN) to generate an embedding from a set of rotamer-based amino acid identities and candidate 3-dimensional C$\\alpha$ locations. Starting from this embedding, we use a bidirectional long short-term memory (LSTM) module to order and label the candidate identities and atomic locations consistent with the input protein sequence to obtain a structural model. Our approach paves the way for determining protein structures from cryo-EM densities at a fraction of the time of existing approaches and without the need for human intervention.","url_abs":"https://arxiv.org/abs/2007.06847v3","url_pdf":"https://arxiv.org/pdf/2007.06847v3.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"sequence-guided-protein-structure","repo_url":"https://github.com/leeneil/structure-generator","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":null,"task_name":"Cryogenic Electron Microscopy (cryo-EM)"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}