ArticleNucleic acids research2015
pyDockSAXS: protein-protein complex structure by SAXS and computational docking.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Using AlphaFold and Symmetrical Docking to Predict Protein-Protein Interactions for Exploring Potential Crystallization Conditions.Proteins · 2025Article
- HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.Nucleic acids research · 2025Article
- Structural basis of CDNF interaction with the UPR regulator GRP78.Nature communications · 2024Article
- Reconstruction of 3D density from solution scattering.Methods in enzymology · 2023Article
- Protein-protein interaction prediction methods: from docking-based to AI-based approaches.Biophysical reviews · 2022Review
- Evolving Experimental Techniques for Structure-Based Drug Design.The journal of physical chemistry. B · 2022Review
- Recent advances in structural characterization of biomacromolecules in foodsFrontiers in nutrition · 2022Review
- Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy.Analytical chemistry · 2021Article
- Conjuring up a ghost: structural and functional characterization of FhuF, a ferric siderophore reductase from E. coli.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- SAXSDom: Modeling multidomain protein structures using small-angle X-ray scattering data.Proteins · 2020Article
- The HDOCK server for integrated protein-protein docking.Nature protocols · 2020Article
- Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Structural Adaptation in Its Orphan Domain Engenders Betaglycan with an Alternate Mode of Growth Factor Binding Relative to Endoglin.Structure (London, England : 1993) · 2019Article
- HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA.Nucleic acids research · 2019Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- What method to use for protein-protein docking?Current opinion in structural biology · 2019Review
- Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.International journal of molecular sciences · 2018Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Structural characterization of protein-protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein-protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein-protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.
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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.