ArticleJournal of structural biology2011
Macromolecular docking restrained by a small angle X-ray scattering profile.
Article in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Bacterial targeting of the neutrophil inhibitory receptor LILRB3 to evade antibody immunity.Nature communications · 2026Article
- Structural basis of the protein kinase PKN1 HR1 domain oligomerization and differential regulation by RhoA and Rac1.The Journal of biological chemistry · 2026Article
- Calcium modulates the tethering of BCOR-PRC1.1 enzymatic core to KDM2B via liquid-liquid phase separation.Communications biology · 2024Article
- Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2.bioRxiv : the preprint server for biology · 2023Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Recent advances in structural characterization of biomacromolecules in foodsFrontiers in nutrition · 2022Review
- A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.Biophysical journal · 2021Article
- Recent Developments in Data-Assisted Modeling of Flexible Proteins.Frontiers in molecular biosciences · 2021Review
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Karyopherin Kap114p-mediated trans-repression controls ribosomal gene expression under saline stress.EMBO reports · 2020Article
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Archiving and disseminating integrative structure models.Journal of biomolecular NMR · 2019Article
- Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis.Biochemistry · 2019Article
- Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Integrative structure modeling with the Integrative Modeling Platform.Protein science : a publication of the Protein Society · 2018Article
- Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics.Archives of biochemistry and biophysics · 2017Review
- Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The ClusPro web server for protein-protein docking.Nature protocols · 2017Article
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Authors and funding
3 authors.
Funding
Abstract
While many structures of single protein components are becoming available, structural characterization of their complexes remains challenging. Methods for modeling assembly structures from individual components frequently suffer from large errors, due to protein flexibility and inaccurate scoring functions. However, when additional information is available, it may be possible to reduce the errors and compute near-native complex structures. One such type of information is a small angle X-ray scattering (SAXS) profile that can be collected in a high-throughput fashion from a small amount of sample in solution. Here, we present an efficient method for protein-protein docking with a SAXS profile (FoXSDock): generation of complex models by rigid global docking with PatchDock, filtering of the models based on the SAXS profile, clustering of the models, and refining the interface by flexible docking with FireDock. FoXSDock is benchmarked on 124 protein complexes with simulated SAXS profiles, as well as on 6 complexes with experimentally determined SAXS profiles. When induced fit is less than 1.5Å interface C(α) RMSD and the fraction residues of missing from the component structures is less than 3%, FoXSDock can find a model close to the native structure within the top 10 predictions in 77% of the cases; in comparison, docking alone succeeds in only 34% of the cases. Thus, the integrative approach significantly improves on molecular docking alone. The improvement arises from an increased resolution of rigid docking sampling and more accurate scoring.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.