{"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/prodconn-server-a-web-server-for-protein","title":"ProDCoNN-server: a web server for protein sequence prediction and design from a three-dimensional structure","arxiv_id":null,"date":"2021-04-11","proceeding":"bioRxiv 2021 4","authors":["Yuan Zhang","Arunima Mandal","Kevin Cui","Xiuwen Liu","Jinfeng Zhang"],"abstract":"We present ProDCoNN-server, a web server for protein sequence design and prediction from a given protein structure. The server is based on a previously developed deep learning model for protein design, ProDCoNN, which achieved state-of-the-art performance when tested on large numbers of test proteins and benchmark datasets. The prediction is very fast compared with other protein sequence prediction servers - it takes only a few minutes for a query protein on average. Two models could be selected for different purposes: BBO for full sequence prediction, extendable for multiple sequence generation, and BBS for single position prediction with the type of other residues known. ProDCoNN-server outputs the predicted sequence and the probability matrix for each amino acid at each predicted residue. The probability matrix can also be visualized as a sequence logos figure (BBO) or probability distribution plot (BBS). The server is available at: https://prodconn.stat.fsu.edu/.","url_abs":"https://www.biorxiv.org/content/10.1101/2021.11.04.467289v1.abstract","url_pdf":"https://www.biorxiv.org/content/10.1101/2021.11.04.467289v1.full.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":"prodconn-server-a-web-server-for-protein","repo_url":"https://github.com/amp1590/protein_design","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"prediction","task_name":"Prediction"},{"task_slug":"protein-design","task_name":"Protein Design"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}