ArticleStructure (London, England : 1993)2017
Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.
Article in Structure (London, England : 1993), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Superwater as a generative AI framework to predict water molecule positions on protein structures.Communications chemistry · 2025Article
- Integrating diverse experimental information to assist protein complex structure prediction by GRASP.Nature methods · 2025Article
- Computational design of highly signalling-active membrane receptors through solvent-mediated allosteric networks.Nature chemistry · 2025Article
- De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO.Scientific reports · 2023Article
- Energy Profile Bayes and Thompson Optimized Convolutional Neural Network protein structure prediction.Neural computing & applications · 2023Article
- Protein Design: From the Aspect of Water Solubility and Stability.Chemical reviews · 2022Review
- Intermolecular Mechanism and Dynamic Investigation of Avian Influenza H7N9 Virus' Susceptibility to E119V-Substituted Peramivir-Neuraminidase Complex.Molecules (Basel, Switzerland) · 2022Article
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
- Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane.Biophysical journal · 2020Article
- A lipophilicity-based energy function for membrane-protein modelling and design.PLoS computational biology · 2019Article
- SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics (Oxford, England) · 2019Article
- Reprogramming G protein coupled receptor structure and function.Current opinion in structural biology · 2018Review
- Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation.The journal of physical chemistry. B · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Solvent molecules interact intimately with proteins and can profoundly regulate their structure and function. However, accurately and efficiently modeling protein solvation effects at the molecular level has been challenging. Here, we present a method that improves the atomic-level modeling of soluble and membrane protein structures and binding by efficiently predicting de novo protein-solvent molecule interactions. The method predicted with unprecedented accuracy buried water molecule positions, solvated protein conformations, and challenging mutational effects on protein binding. When applied to homology modeling, solvent-bound membrane protein structures, pockets, and cavities were recapitulated with near-atomic precision even from distant homologs. Blindly refined atomic-level structures of evolutionary distant G protein-coupled receptors imply strikingly different functional roles of buried solvent between receptor classes. The method should prove useful for refining low-resolution protein structures, accurately modeling drug-binding sites in structurally uncharacterized receptors, and designing solvent-mediated protein catalysis, recognition, ligand binding, and membrane protein signaling.
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