Thanks to visit codestin.com
Credit goes to www.biomedcentral.com

Skip to main content
This website is moving to Springer Nature Link.

Computational inference of protein conformations and interactions

Guest Editors

Jacob D. Durrant, PhD, University of Pittsburgh, USA
Tatiana Galochkina, PhD, University Paris Cité & INSERM, France
Balachandran Manavalan, PhD, Sungkyunkwan University, South Korea


BMC Biology called for submissions to our Collection on Computational inference of protein conformations and interactions.

This Collection welcomed submissions on the prediction of protein-protein interactions, protein/small-molecule interactions, and binding motifs. Additionally, we encouraged submissions focusing on conformational dynamics and intrinsically disordered regions (IDRs). We welcomed manuscripts describing the application of machine learning and deep learning to address these important questions.

Meet the Guest Editors

Back to top

Jacob D. Durrant, PhD, University of Pittsburgh, USA

Dr Jacob D. Durrant is an Associate Professor of Biological Sciences at the University of Pittsburgh. His research focuses on developing and applying computer-aided drug design (CADD) techniques to advance early-stage ligand discovery. Dr Durrant’s lab develops machine-learning and big-data tools to predict ligand poses and affinities, as well as simulation tools to study protein motions that impact ligand binding. Using these and related tools, he has discovered over seventy validated protein-binding small molecules targeting more than a dozen disease-relevant proteins. Dr Durrant’s work also aims to encourage broad tool adoption through open-source software development and an emphasis on usability.

Tatiana Galochkina, PhD, University Paris Cité & INSERM, France

Dr Tatiana Galochkina holds a PhD in Applied Mathematics from Université Lyon 1 and PhD in Mathematical and Physical Sciences from Lomonosov Moscow State University, and currently works as an Associate Professor in bioinformatics at Université Paris Cité, team DSIMB. Her research is focused on the analysis and prediction of protein dynamics and interactions with other molecules, in particular, with carbohydrates, using a combination of molecular modeling and machine learning approaches. Finally, Dr Galochkina is an author and teaches two master courses on machine learning applications to biological data at Université Paris Cité.

Balachandran Manavalan, PhD, Sungkyunkwan University, South Korea

Dr Balachandran Manavalan is an Assistant Professor at the Department of Integrative Biotechnology, Sungkyunkwan University (SKKU). He earned his PhD in Computational Biology from Ajou University in 2011 and subsequently served as a research fellow and research assistant professor at Korea Institute for Advanced Study and Ajou University School of Medicine. He established his research group at SKKU’s Department of Integrative Biotechnology in 2022. Dr Manavalan's research focuses on artificial intelligence, bioinformatics, machine learning, big data, proteomics, and functional genomics. His remarkable research achievements have placed him the top 2% highly cited researcher for the past four consecutive years, according to the Stanford University data.

About the Collection

BMC Biology is calling for submissions to our Collection on Computational inference of protein conformations and interactions.

With advancements in computational techniques and the exponential growth of available biological data, the prediction of protein conformational dynamics and interactions with diverse molecular targets has garnered significant attention. In silico tools can identify binding motifs and predict protein interactions with other proteins and small-molecule ligands (e.g., drugs, lipids, sugars, nucleotides), driving advancements in drug discovery and personalized medicine. 

This Collection welcomes submissions on the prediction of protein-protein interactions, protein/small-molecule interactions, and binding motifs. Additionally, we encourage submissions focusing on conformational dynamics and intrinsically disordered regions (IDRs). We welcome manuscripts describing the application of machine learning and deep learning to address these important questions.

Topics may include, but are not limited to:

  • Novel methods for predicting protein/protein and protein/small-molecule interactions
  • Analyses of protein interaction networks and pathways
  • Prediction of protein structure and conformational changes
  • Analysis of sequence and structural binding motifs
  • Reverse virtual screening approaches for identifying potential drug targets
  • Prediction and characterization of Intrinsically Disordered Regions (IDRs)


Image credit: © [M] Christoph Burgstedt / Getty Images / iStock

  1. Non-histone lysine acetylation is a widespread protein post-translational modification that regulates almost all key cellular processes, and its dysregulation is closely associated with various human diseases....

    Authors: Yuqing Geng, Hao Luo and Feng Gao
    Citation: BMC Biology 2025 23:311
  2. Bacterial infections rank as the second leading cause of death globally, with virulence factors (VFs) being crucial to their pathogenicity. Predicting VFs accurately can uncover mechanisms of bacterial disease...

    Authors: Yitong Liu, Xin Cao, Jiani Li, Tao Li, Juanjuan Li, Xiang Ma, Xue Chi, Yanqiong Tang, Zhu Liu and Hong Li
    Citation: BMC Biology 2025 23:307
  3. Protein-protein interactions (PPIs) play a critical role in essential biological processes such as signal transduction, enzyme activity regulation, cytoskeletal structure, immune responses, and gene regulation...

    Authors: Feng Wang, Jinming Chu, Liyan Shen and Shan Chang
    Citation: BMC Biology 2025 23:253
  4. Learning-based methods have recently demonstrated strong potential in predicting drug-protein interactions (DPIs). However, existing approaches often fail to achieve accurate predictions on real-world imbalanc...

    Authors: Yanfei Li, Xiran Chen, Shuqin Wang and Jinmao Wei
    Citation: BMC Biology 2025 23:243
  5. Prediction of protein–protein interactions (PPIs) is fundamental for identifying drug targets and understanding cellular processes. The rapid growth of PPI studies necessitates the development of efficient and...

    Authors: Tao Tang, Taiguang Shen, Jing Jiang, Weizhuo Li, Peng Wang, Sisi Yuan, Xiaofeng Cao and Yuansheng Liu
    Citation: BMC Biology 2025 23:236
  6. Drug-target interaction (DTI) refers to the specific mechanisms by which drug molecules interact with biological targets within a biological system. Computational methods are widely employed for DTI prediction...

    Authors: Yuqing Qian, Xin Zhang, Yizheng Wang, Quan Zou, Chen Cao, Yijie Ding and Xiaoyi Guo
    Citation: BMC Biology 2025 23:225
  7. Accurate identification of anti-inflammatory peptides (AIPs) is crucial for drug development and inflammatory disease treatment. However, the short length and limited informational content of peptide sequences...

    Authors: Chengzhi Xie, Yijie Wei, Xinwei Luo, Huan Yang, Hongyan Lai, Fuying Dao, Juan Feng and Hao Lv
    Citation: BMC Biology 2025 23:212
  8. Diabetes is a global metabolic disease that urgently calls for the development of new and effective therapeutic agents. Anti-diabetic peptides (ADPs) have emerged as a research hotspot due to their therapeutic...

    Authors: Xueqin Xie, Changchun Wu, Yixuan Qi, Shanghua Liu, Jian Huang, Hao Lyu, Fuying Dao and Hao Lin
    Citation: BMC Biology 2025 23:210
  9. Antimicrobial peptide (AMP) prediction has been extensively studied in recent years. However, many existing models do not fully leverage the intrinsic chemical structures of AMPs, such as atomic composition an...

    Authors: Yongcheng He, Xu Song, Hongping Wan and Xinghong Zhao
    Citation: BMC Biology 2025 23:184
  10. Dipeptidyl peptidase-4 (DPP4) is considered a crucial enzyme in type 2 diabetes (T2D) treatment, targeted by inhibitors due to its role in cleaving glucagon-like peptide-1 (GLP-1). In this study, a novel DPP4 ...

    Authors: Yi He, Yan Zhang, Minghao Liu, Jiaying Li, Wannan Li and Weiwei Han
    Citation: BMC Biology 2025 23:173
  11. Accurately identifying targets not only guides treatments for diseases with unclear pathogenic mechanisms, but also reduces pharmaceutical costs and accelerates drug development timelines. However, the primary...

    Authors: Xin Zeng, Guang-Peng Su, Wen-Feng Du, Bei Jiang, Yi Li and Zi-Zhong Yang
    Citation: BMC Biology 2025 23:168
  12. Understanding protein-molecular interaction is crucial for unraveling the mechanisms underlying diverse biological processes. Machine learning (ML) techniques have been extensively employed in predicting these...

    Authors: Pengpai Li, Bowen Shao, Guoqing Zhao and Zhi-Ping Liu
    Citation: BMC Biology 2025 23:123
  13. Drug-target binding affinity (DTA) prediction can accelerate the drug screening process, and deep learning techniques have been used in all facets of drug research. Affinity prediction based on deep learning m...

    Authors: Xun Wang, Zhijun Xia, Runqiu Feng, Tongyu Han, Hanyu Wang, Wenqian Yu and Xingguang Wang
    Citation: BMC Biology 2025 23:120
  14. Lactylation is a newly discovered type of post-translational modification, primarily occurring on lysine (K) residues of both histones and non-histones to exert diverse effects on target proteins. Research has...

    Authors: Hongyan Lai, Diyu Luo, Mi Yang, Tao Zhu, Huan Yang, Xinwei Luo, Yijie Wei, Sijia Xie, Feitong Hong, Kunxian Shu, Fuying Dao and Hui Ding
    Citation: BMC Biology 2025 23:95
  15. RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.

    Authors: Xiaoyong Pan, Yi Fang, Xiaojian Liu, Xiaoyu Guo and Hong-Bin Shen
    Citation: BMC Biology 2025 23:74
  16. Cyclic peptides, known for their high binding affinity and low toxicity, show potential as innovative drugs for targeting “undruggable” proteins. However, their therapeutic efficacy is often hindered by poor m...

    Authors: Zixu Wang, Yangyang Chen, Yifan Shang, Xiulong Yang, Wenqiong Pan, Xiucai Ye, Tetsuya Sakurai and Xiangxiang Zeng
    Citation: BMC Biology 2025 23:63
  17. Poliovirus receptor (PVR) and its receptor system, including TIGIT, CD226, and CD96, play a pivotal role in orchestrating tumor immune evasion. Upon engagement with PVR on tumor cells, CD96 exerts inhibitory e...

    Authors: Xiangrui Zhang, Lihan Zhang, Beibei Li, Qingchao Wang, Peixin Chen, Ranran Shi, Xiuman Zhou, Xiaoshuang Niu, Wenjie Zhai, Yahong Wu, Wenhui Shen, Xiaowen Zhou and Wenshan Zhao
    Citation: BMC Biology 2025 23:27
  18. For decades, KRAS has always been a huge challenge to the field of drug discovery for its significance in cancer progression as well as its difficulties in being targeted as an “undruggable” protein. KRAS regu...

    Authors: Sanan Wu, Xiaoyang Gao, Di Wu, Lu Liu, Han Yao, Xiangjun Meng, Xianglei Zhang and Fang Bai
    Citation: BMC Biology 2024 22:264
  19. Accurate prediction of compound-protein interaction (CPI) plays a crucial role in drug discovery. Existing data-driven methods aim to learn from the chemical structures of compounds and proteins yet ignore the...

    Authors: Wen Tao, Xuan Lin, Yuansheng Liu, Li Zeng, Tengfei Ma, Ning Cheng, Jing Jiang, Xiangxiang Zeng and Sisi Yuan
    Citation: BMC Biology 2024 22:248
  20. Accurately identifying drug-target affinity (DTA) plays a pivotal role in drug screening, design, and repurposing in pharmaceutical industry. It not only reduces the time, labor, and economic costs associated ...

    Authors: Xin Zeng, Kai-Yang Zhong, Pei-Yan Meng, Shu-Juan Li, Shuang-Qing Lv, Meng-Liang Wen and Yi Li
    Citation: BMC Biology 2024 22:182
  21. Identification of potential drug-target interactions (DTIs) with high accuracy is a key step in drug discovery and repositioning, especially concerning specific drug targets. Traditional experimental methods f...

    Authors: Yongdi Zhu, Chunhui Ning, Naiqian Zhang, Mingyi Wang and Yusen Zhang
    Citation: BMC Biology 2024 22:156
  22. Metabolite-associated cell communications play critical roles in maintaining human biological function. However, most existing tools and resources focus only on ligand-receptor interaction pairs where both par...

    Authors: Yuncong Zhang, Yu Yang, Liping Ren, Meixiao Zhan, Taoping Sun, Quan Zou and Yang Zhang
    Citation: BMC Biology 2024 22:152

Submission Guidelines

Back to top

This Collection welcomes submission of original Research Articles. Should you wish to submit a different article type, please read our submission guidelines to confirm that type is accepted by the journal. To submit your manuscript to this Collection, please use our online submission system. During the submission process you will be asked whether you are submitting to a Collection, please select "Computational inference of protein conformations and interactions" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Editors have competing interests is handled by another Editorial Board Member who has no competing interests.