ArticleBioinformatics (Oxford, England)2017
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- USP1 driven mitotic dysregulation and PLK1 stabilization confer Lenvatinib resistance in hepatocellular carcinoma.Journal of experimental & clinical cancer research : CR · 2026Article
- A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models.Biomolecules · 2024Review
- Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies.Current atherosclerosis reports · 2023Review
- MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations.Biomolecules · 2023Article
- Improving classification of correct and incorrect protein-protein docking models by augmenting the training set.Bioinformatics advances · 2023Article
- Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants.Protein science : a publication of the Protein Society · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- A random forest classifier for protein-protein docking models.Bioinformatics advances · 2022Article
- The use of predictive models to develop chromatography-based purification processes.Frontiers in bioengineering and biotechnology · 2022Review
- Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.Journal of chemical theory and computation · 2021Article
- An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.Structure (London, England : 1993) · 2021Article
- Improved cluster ranking in protein-protein docking using a regression approach.Computational and structural biotechnology journal · 2021Article
- Docking approaches for modeling multi-molecular assemblies.Current opinion in structural biology · 2020Review
- Performance and Its Limits in Rigid Body Protein-Protein Docking.Structure (London, England : 1993) · 2020Article
- iScore: a novel graph kernel-based function for scoring protein-protein docking models.Bioinformatics (Oxford, England) · 2020Article
- What method to use for protein-protein docking?Current opinion in structural biology · 2019Review
- SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics (Oxford, England) · 2019Article
- Refinement of protein-protein complexes in contact map space with metadynamics simulations.Proteins · 2019Article
- Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes.Scientific reports · 2018Article
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9 authors.
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Abstract
motivationIn order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction.
resultsAtomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. AVAILABILITY AND IMPLEMENTATION: IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. CONTACT: moal@ebi.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.