ArticleProteins2014
Blind prediction of interfacial water positions in CAPRI.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Blind prediction of complex water and ion ensembles around RNA in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Bacterial warfare is associated with virulence and antimicrobial resistance.Nature communications · 2025Article
- Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.Proteins · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Protein-protein interaction prediction methods: from docking-based to AI-based approaches.Biophysical reviews · 2022Review
- Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens.Scientific reports · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking.PloS one · 2022Article
- Article
- Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants.PLoS computational biology · 2021Article
- Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination.PLoS computational biology · 2020Article
- Article
- The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.Frontiers in molecular biosciences · 2018Article
- Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.Structure (London, England : 1993) · 2017Article
- Performance of ZDOCK and IRAD in CAPRI rounds 28-34.Proteins · 2017Article
- Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions.Proteins · 2017Article
- FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility.Proteins · 2017Article
- Article
- On the ability of molecular dynamics simulation and continuum electrostatics to treat interfacial water molecules in protein-protein complexes.Scientific reports · 2016Article
- Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.Proteins · 2016Article
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Authors and funding
58 authors.
Funding
Abstract
We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models-a very good docking performance per se-only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 Å, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced high-quality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein-water interactions and their role in stabilizing protein complexes.
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