{"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/helixfold-single-msa-free-protein-structure","title":"HelixFold-Single: MSA-free Protein Structure Prediction by Using Protein Language Model as an Alternative","arxiv_id":"2207.13921","date":"2022-07-28","proceeding":null,"authors":["Xiaomin Fang","Fan Wang","Lihang Liu","Jingzhou He","Dayong Lin","Yingfei Xiang","Xiaonan Zhang","Hua Wu","Hui Li","Le Song"],"abstract":"AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from the homologous sequences. Nonetheless, searching MSAs from protein databases is time-consuming, usually taking dozens of minutes. Consequently, we attempt to explore the limits of fast protein structure prediction by using only primary sequences of proteins. HelixFold-Single is proposed to combine a large-scale protein language model with the superior geometric learning capability of AlphaFold2. Our proposed method, HelixFold-Single, first pre-trains a large-scale protein language model (PLM) with thousands of millions of primary sequences utilizing the self-supervised learning paradigm, which will be used as an alternative to MSAs for learning the co-evolution information. Then, by combining the pre-trained PLM and the essential components of AlphaFold2, we obtain an end-to-end differentiable model to predict the 3D coordinates of atoms from only the primary sequence. HelixFold-Single is validated in datasets CASP14 and CAMEO, achieving competitive accuracy with the MSA-based methods on the targets with large homologous families. Furthermore, HelixFold-Single consumes much less time than the mainstream pipelines for protein structure prediction, demonstrating its potential in tasks requiring many predictions. The code of HelixFold-Single is available at https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold-single, and we also provide stable web services on https://paddlehelix.baidu.com/app/drug/protein-single/forecast.","url_abs":"https://arxiv.org/abs/2207.13921v3","url_pdf":"https://arxiv.org/pdf/2207.13921v3.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":"helixfold-single-msa-free-protein-structure","repo_url":"https://github.com/PaddlePaddle/PaddleHelix","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"paddle","reach":{"status":"ok","spdx":"NOASSERTION"}}],"tasks":[{"task_slug":"language-modeling","task_name":"Language Modeling"},{"task_slug":"language-modelling","task_name":"Language Modelling"},{"task_slug":"protein-language-model","task_name":"Protein Language Model"},{"task_slug":"protein-structure-prediction","task_name":"Protein Structure Prediction"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2207.13921","atlas_url":"https://app.syntology.ai/?focus=2207.13921","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}