ArticleScientific reports2018
A Novel Geometry-Based Approach to Infer Protein Interface Similarity.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Using AlphaFold and Symmetrical Docking to Predict Protein-Protein Interactions for Exploring Potential Crystallization Conditions.Proteins · 2025Article
- Database-Driven Identification of Structurally Similar Protein-Protein Interfaces.Journal of chemical information and modeling · 2024Article
- Surface ID: a geometry-aware system for protein molecular surface comparison.Bioinformatics (Oxford, England) · 2023Article
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- An overview of descriptors to capture protein properties - Tools and perspectives in the context of QSAR modeling.Computational and structural biotechnology journal · 2023Review
- Topsy-Turvy: integrating a global view into sequence-based PPI prediction.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The protein interface is key to understand protein function, providing a vital insight on how proteins interact with each other and with other molecules. Over the years, many computational methods to compare protein structures were developed, yet evaluating interface similarity remains a very difficult task. Here, we present PatchBag - a geometry based method for efficient comparison of protein surfaces and interfaces. PatchBag is a Bag-Of-Words approach, which represents complex objects as vectors, enabling to search interface similarity in a highly efficient manner. Using a novel framework for evaluating interface similarity, we show that PatchBag performance is comparable to state-of-the-art alignment-based structural comparison methods. The great advantage of PatchBag is that it does not rely on sequence or fold information, thus enabling to detect similarities between interfaces in unrelated proteins. We propose that PatchBag can contribute to reveal novel evolutionary and functional relationships between protein interfaces.
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Registered trials
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