ArticleInternational journal of molecular sciences2010
SwarmDock and the use of normal modes in protein-protein docking.
Article in International journal of molecular sciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Energy Measures as Biomarkers of SARS-CoV-2 Variants and Receptors.Bioengineering (Basel, Switzerland) · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Article
- A comprehensive survey of scoring functions for protein docking models.BMC bioinformatics · 2025Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Flexible protein-protein docking with a multitrack iterative transformer.Protein science : a publication of the Protein Society · 2024Article
- ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information.Communications biology · 2024Article
- Assessment of Protein-Protein Docking Models Using Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Docking Foundations: From Rigid to Flexible Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Approaches to Backbone Flexibility in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Free-Docking and Template-Based Docking: Physics Versus Knowledge-Based Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α.Scientific reports · 2023Article
- MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations.Biomolecules · 2023Article
- Modeling Protein Complexes and Molecular Assemblies Using Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Local Normal Mode Analysis for Fast Loop Conformational Sampling.Journal of chemical information and modeling · 2022Article
- Induced fit with replica exchange improves protein complex structure prediction.PLoS computational biology · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Ensemble learning from ensemble docking: revisiting the optimum ensemble size problem.Scientific reports · 2022Article
- Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies.Frontiers in molecular biosciences · 2022Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
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Abstract
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
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Registered trials
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