New benchmark metrics for protein-protein docking methods.
Mu Gao,Jeffrey Skolnick +1 more
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TLDR
This work focuses on characterizing the similarity of the interfaces of the complex and introduces two scoring functions, the interfacial Template Modeling score (iTM‐score) and the Interface Similarity score (IS‐score), which identifies models whose significance was previously underestimated.Abstract:
With the development of many computational methods that predict the structural models of protein-protein complexes, there is a pressing need to benchmark their performance. As was the case for protein monomers, assessing the quality of models of protein complexes is not straightforward. An effective scoring scheme should be able to detect substructure similarity and estimate its statistical significance. Here, we focus on characterizing the similarity of the interfaces of the complex and introduce two scoring functions. The first, the interfacial Template Modeling score (iTM-score), measures the geometric distance between the interfaces, while the second, the Interface Similarity score (IS-score), evaluates their residue-residue contact similarity in addition to their geometric similarity. We first demonstrate that the IS-score is more suitable for assessing docking models than the iTM-score. The IS-score is then validated in a large-scale benchmark test on 1562 dimeric complexes. Finally, the scoring function is applied to evaluate docking models submitted to the Critical Assessment of Prediction of Interactions (CAPRI) experiments. While the results according to the new scoring scheme are generally consistent with the original CAPRI assessment, the IS-score identifies models whose significance was previously underestimated.read more
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Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology
Martino Bertoni,Martino Bertoni,Florian Kiefer,Florian Kiefer,Marco Biasini,Marco Biasini,Lorenza Bordoli,Lorenza Bordoli,Torsten Schwede,Torsten Schwede +9 more
TL;DR: A description of protein-protein interface conservation as a function of evolutionary distance to reduce the noise in deep multiple sequence alignments and a distance measure to structurally compare homologous multimeric protein complexes are defined.
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DockQ: A Quality Measure for Protein-Protein Docking Models.
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TL;DR: DockQ is presented, a continuous protein-protein docking model quality measure derived by combining Fnat, LRMS, and iRMS to a single score in the range [0, 1] that can be used to assess the quality of protein docking models.
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APoc: large-scale identification of similar protein pockets
Mu Gao,Jeffrey Skolnick +1 more
TL;DR: This work introduces a computational method, APoc (Alignment of Pockets), for the large-scale, sequence order-independent, structural comparison of protein pockets, and demonstrates that APoc has better performance than the geometric hashing-based method SiteEngine.
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AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
TL;DR: In this article , the same neural network models from AlphaFold2 developed for single protein sequences can be adapted to predict the structures of multimeric protein complexes without retraining.
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Mapping monomeric threading to protein-protein structure prediction.
TL;DR: A novel strategy SPRING is proposed to identify complexes by mapping monomeric threading alignments to protein-protein interactions based on the original oligomer entries in the PDB, which does not rely on library construction and increases the efficiency and quality of complex template recognitions.
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