ArticlePLoS computational biology2020
Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 63 citations in OpenAlex.
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- Distinct energetic blueprints diversify function of conserved protein folds.Nature chemistry · 2026Article
- A Generative Neuro-Symbolic AI for Protein Sequence Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- Chemical Profiling, Pharmacological Activities, and Toxicity Assessment ofFood science & nutrition · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- A Kv2 inhibitor combination reveals native neuronal conductances consistent with Kv2/KvS heteromers.eLife · 2025Article
- Estimating Absolute Protein-Protein Binding Free Energies by a Super Learner Model.Journal of chemical information and modeling · 2025Article
- Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm.Biophysics and physicobiology · 2025Article
- An artificial intelligence accelerated virtual screening platform for drug discovery.Nature communications · 2024Article
- Complete combinatorial mutational enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity.Protein science : a publication of the Protein Society · 2024Article
- MolModa: accessible and secure molecular docking in a web browser.Nucleic acids research · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.PLoS computational biology · 2024Article
- Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.PLoS computational biology · 2024Article
- HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Water Molecule Positions for Protein Structures.Journal of chemical information and modeling · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.bioRxiv : the preprint server for biology · 2024Article
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO.Scientific reports · 2023Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Highly coordinated water molecules are frequently an integral part of protein-protein and protein-ligand interfaces. We introduce an updated energy model that efficiently captures the energetic effects of these ordered water molecules on the surfaces of proteins. A two-stage method is developed in which polar groups arranged in geometries suitable for water placement are first identified, then a modified Monte Carlo simulation allows highly coordinated waters to be placed on the surface of a protein while simultaneously sampling amino acid side chain orientations. This "semi-explicit" water model is implemented in Rosetta and is suitable for both structure prediction and protein design. We show that our new approach and energy model yield significant improvements in native structure recovery of protein-protein and protein-ligand docking discrimination tests.
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