ArticleJournal of molecular biology2018
Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.
Article in Journal of molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome fragment.Nature communications · 2025Article
- Mapping the interaction surface between CaNature communications · 2025Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry.Cell reports methods · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches.International journal of molecular sciences · 2021Review
- Advances to tackle backbone flexibility in protein docking.Current opinion in structural biology · 2021Review
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- Article
- High-density chemical cross-linking for modeling protein interactions.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Proper evaluation of chemical cross-linking-based spatial restraints improves the precision of modeling homo-oligomeric protein complexes.BMC bioinformatics · 2019Article
- What method to use for protein-protein docking?Current opinion in structural biology · 2019Review
- Chemical cross-linking with mass spectrometry: a tool for systems structural biology.Current opinion in chemical biology · 2019Review
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Authors and funding
8 authors.
Funding
Abstract
Ab initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 19 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or void-volume distance. For most test cases, the rank of the top-scoring near-native prediction was improved by at least twofold compared with docking without the cross-link information, and the success rate for the top 5 predictions nearly tripled. Our results demonstrate the delicate balance between retaining correct predictions and eliminating false positives. Several test cases had multiple components with distinct interfaces, and we present an approach for assigning cross-links to the interfaces. Employing the symmetry information for these cases further improved the performance of complex structure prediction.
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Registered trials
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