ArticleProceedings of the National Academy of Sciences of the United States of America2010
Protein interface conservation across structure space.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- Using multiscale molecular dynamics simulations to explore the fusion machinery underlying neurotransmitter release.Quarterly reviews of biophysics · 2025Review
- Genome-scale annotation of protein binding sites via language model and geometric deep learning.eLife · 2024Article
- SENSDeep: An Ensemble Deep Learning Method for Protein-Protein Interaction Sites Prediction.Interdisciplinary sciences, computational life sciences · 2023Article
- Artificial Intelligence and Machine Learning Technology Driven Modern Drug Discovery and Development.International journal of molecular sciences · 2023Review
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Oligomeric interactions maintain active-site structure in a noncooperative enzyme family.The EMBO journal · 2022Article
- ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction.Nature methods · 2022Article
- AF2Complex predicts direct physical interactions in multimeric proteins with deep learning.Nature communications · 2022Article
- Machine Learning in Drug Discovery: A Review.Artificial intelligence review · 2022Article
- MENSAdb: a thorough structural analysis of membrane protein dimers.Database : the journal of biological databases and curation · 2021Article
- How to choose templates for modeling of protein complexes: Insights from benchmarking template-based docking.Proteins · 2020Article
- Predicting Protein-Protein Interactions from Matrix-Based Protein Sequence Using Convolution Neural Network and Feature-Selective Rotation Forest.Scientific reports · 2019Article
- Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions.PloS one · 2019Article
- Interface-Based Structural Prediction of Novel Host-Pathogen Interactions.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery.Molecules (Basel, Switzerland) · 2018Review
- SWISS-MODEL: homology modelling of protein structures and complexes.Nucleic acids research · 2018Article
- Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues.Pharmaceuticals (Basel, Switzerland) · 2018Article
- Protein-protein interaction specificity is captured by contact preferences and interface composition.Bioinformatics (Oxford, England) · 2018Article
- Dockground: A comprehensive data resource for modeling of protein complexes.Protein science : a publication of the Protein Society · 2018Article
- Structure-based prediction of ligand-protein interactions on a genome-wide scale.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
19 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
With the advent of Systems Biology, the prediction of whether two proteins form a complex has become a problem of increased importance. A variety of experimental techniques have been applied to the problem, but three-dimensional structural information has not been widely exploited. Here we explore the range of applicability of such information by analyzing the extent to which the location of binding sites on protein surfaces is conserved among structural neighbors. We find, as expected, that interface conservation is most significant among proteins that have a clear evolutionary relationship, but that there is a significant level of conservation even among remote structural neighbors. This finding is consistent with recent evidence that information available from structural neighbors, independent of classification, should be exploited in the search for functional insights. The value of such structural information is highlighted through the development of a new protein interface prediction method, PredUs, that identifies what residues on protein surfaces are likely to participate in complexes with other proteins. The performance of PredUs, as measured through comparisons with other methods, suggests that relationships across protein structure space can be successfully exploited in the prediction of protein-protein interactions.
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