{"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/esm-nbr-fast-and-accurate-nucleic-acid","title":"ESM-NBR: fast and accurate nucleic acid-binding residue prediction via protein language model feature representation and multi-task learning","arxiv_id":"2312.00842","date":"2023-12-01","proceeding":null,"authors":["Wenwu Zeng","Dafeng Lv","Wenjuan Liu","Shaoliang Peng"],"abstract":"Protein-nucleic acid interactions play a very important role in a variety of biological activities. Accurate identification of nucleic acid-binding residues is a critical step in understanding the interaction mechanisms. Although many computationally based methods have been developed to predict nucleic acid-binding residues, challenges remain. In this study, a fast and accurate sequence-based method, called ESM-NBR, is proposed. In ESM-NBR, we first use the large protein language model ESM2 to extract discriminative biological properties feature representation from protein primary sequences; then, a multi-task deep learning model composed of stacked bidirectional long short-term memory (BiLSTM) and multi-layer perceptron (MLP) networks is employed to explore common and private information of DNA- and RNA-binding residues with ESM2 feature as input. Experimental results on benchmark data sets demonstrate that the prediction performance of ESM2 feature representation comprehensively outperforms evolutionary information-based hidden Markov model (HMM) features. Meanwhile, the ESM-NBR obtains the MCC values for DNA-binding residues prediction of 0.427 and 0.391 on two independent test sets, which are 18.61 and 10.45% higher than those of the second-best methods, respectively. Moreover, by completely discarding the time-cost multiple sequence alignment process, the prediction speed of ESM-NBR far exceeds that of existing methods (5.52s for a protein sequence of length 500, which is about 16 times faster than the second-fastest method). A user-friendly standalone package and the data of ESM-NBR are freely available for academic use at: https://github.com/wwzll123/ESM-NBR.","url_abs":"https://arxiv.org/abs/2312.00842v1","url_pdf":"https://arxiv.org/pdf/2312.00842v1.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":"esm-nbr-fast-and-accurate-nucleic-acid","repo_url":"https://github.com/pengsl-lab/esm-nbr","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null},{"paper_slug":"esm-nbr-fast-and-accurate-nucleic-acid","repo_url":"https://github.com/wwzll123/esm-nbr","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"language-modeling","task_name":"Language Modeling"},{"task_slug":"language-modelling","task_name":"Language Modelling"},{"task_slug":"multi-task-learning","task_name":"Multi-Task Learning"},{"task_slug":"multiple-sequence-alignment","task_name":"Multiple Sequence Alignment"},{"task_slug":"protein-language-model","task_name":"Protein Language Model"}],"methods":[{"method_slug":"speed","method_name":"SPEED"}],"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}