The 4th National Conference on Biomolecular Structure Prediction and Modeling was held in Qingdao from June 26 to 29, 2026, with several members of our research group in attendance. Jiajun delivered an oral presentation of our latest work, SteerAF: distogram-based steering of AlphaFold2 toward alternative conformations, and was awarded the second prize for oral reports. Ruihan and Qiushi received the third prize in the poster section. We extend our sincere congratulations to both!
Our latest membrane contact probability (MCP) predictor, PepMCP, has been published in Bioinformatics (link). PepMCP is a novel peptide-tailored model that predicts MCP and identifies membrane-lytic antimicrobial peptides (AMPs). We trained PepMCP on data from more than 500 literature-sourced membrane-lytic AMPs. It leverages coarse-grained molecular dynamics simulations to extract residue-level MCP features for model training. PepMCP can also be used in a binary classification mode, enabling efficient identification of membrane-lytic AMPs. The study also releases MemAMPdb, a curated membrane-lytic AMP database, together with a publicly accessible PepMCP web server, to support global academic research. Several group members participated in the research. Ruihan constructed the model, and Tadsanee ran the large-scale MD simulations. Congratulations!
We are delighted to welcome Dr. Yi Ren to the group. Having earned his PhD, he joins us as a postdoctoral researcher. We look forward to his future contributions. Welcome aboard!
Hongyang and Zhouyu successfully completed their undergraduate thesis defenses on May 29 and June 5, 2026, respectively. Congratulations!
Zhongjie has completed his postdoctoral research and left our group to take up a new role. During his time here, he made outstanding contributions to the development of the membrane-aware anisotropic network model (MCP-ANM). He has joined Beijing Sun-Novo Pharmaceutical Research Co., Ltd. as a director of innovative drug research. We wish him every success in his future career.
Our collaborative study with Prof. Xiao-Wei Chen' lab and Prof. Ning Gao' lab has been published online in Molecular Cell (link). Using MD simulations, we uncovered specific phosphatidylinositol (PI)-binding pockets on the Erlin1/2 complex at the ER membrane luminal leaflet. PI binding is critical for the complex’s stability and assembly. Congratulations to Tadsanee!
Zhongjie's work on membrane protein dynamics has been published in PRX Life (link). The study introduces MCP-ANM, a membrane-aware anisotropic network model that incorporates membrane contact probability (MCP) to better describe membrane-induced constraints in protein dynamics. The method significantly improves flexibility prediction for membrane proteins compared with conventional ANM approaches. By integrating MCP-ANM with perturbation response scanning (PRS), the framework efficiently simulates mechanosensitive gating mechanisms, reproducing both force-from-lipids (e.g., MscS, PIEZO) and force-from-tether (e.g., NOMPC) models. The predicted mechanosensitivity agrees with experimental observations, while requiring only seconds to minutes per system. Congratulations!
Prof. Chen Song, along with YC, Kai, and Jingze, attended the BPS2026 meeting held in San Francisco, USA, from February 21 to 25, 2026. At the conference, they presented and discussed our recent work on ProtRAP-LM, RAPFold, as well as the molecular mechanics studies of the ion channels (including NOMPC and CaV1 channel).
Lei and Kai’s work on ProtRAP-LM has been published in Genom. Proteom. Bioinform. (link). The study introduces ProtRAP-LM, a transformer-based model that uses protein language model embeddings to rapidly and accurately predict membrane contact probability (MCP) and relative accessibility for each residue within a given protein sequence. ProtRAP-LM achieves a speed-up of over 300 times compared to MSA-based MCP predictor, enabling proteome-wide predictions within hours. This facilitates large-scale analysis of challenging membrane protein classes, including single-pass transmembrane proteins, membrane-anchored proteins, and β-sheet-containing membrane proteins. In particular, this study provides a comprehensive list of membrane proteins across 48 proteomes, including 78 potential human membrane proteins, offering a valuable resource for future structural and functional studies. An online server is available at http://www.songlab.cn/ProtRAP-LM/home/. Congratulations!
