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BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix

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Abstract

Protein complex structure prediction is an important problem in computational biology. While significant progress has been made for protein monomers, accurate evaluation of protein complexes remains challenging. Existing assessment methods in CASP, lack dedicated metrics for evaluating complexes. DockQ, a widely used metric, has some limitations. In this study, we propose a novel metric called BDM (Based on Distance difference Matrix) for assessing protein complex prediction structures. Our approach utilizes a distance difference matrix derived from comparing real and predicted protein structures, establishing a linear correlation with Root Mean Square Deviation (RMSD). BDM overcomes limitations associated with receptor-ligand differentiation and eliminates the requirement for structure alignment, making it a more effective and efficient metric. Evaluation of BDM using CASP14 and CASP15 test sets demonstrates superior performance compared to the official CASP scoring. BDM provides accurate and reasonable assessments of predicted protein complexes, wide adoption of BDM has the potential to advance protein complex structure prediction and facilitate related researches across scientific domains. Code is available at http://mialab.ruc.edu.cn/BDMServer/.

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Data availability

The source code and server are available at http://mialab.ruc.edu.cn/BDMServer/. The datasets can be found on the websites mentioned in the “Datasets” section of the main text.

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Acknowledgements

The authors thank the anonymous reviewers for their valuable suggestions. This research was supported by Public Computing Cloud and School of Interdisciplinary Studies, Renmin University of China.

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  1. Jiaqi Zhai and Wenda Wang have contributed equally to this work.

Authors and Affiliations

  1. Institute for Mathematical Sciences, Renmin University of China, Beijing, 100872, China

    Jiaqi Zhai, Wenda Wang, Ranxi Zhao, Daiwen Sun, Da Lu & Xinqi Gong

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  1. Jiaqi Zhai
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  2. Wenda Wang
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  3. Ranxi Zhao
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  4. Daiwen Sun
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  5. Da Lu
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Correspondence to Xinqi Gong.

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Zhai, J., Wang, W., Zhao, R. et al. BDM: An Assessment Metric for Protein Complex Structure Models Based on Distance Difference Matrix. Interdiscip Sci Comput Life Sci (2024). https://doi.org/10.1007/s12539-024-00622-1

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