ArticleACS medicinal chemistry letters2020
ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design.
Article in ACS medicinal chemistry letters, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 24 citations in OpenAlex.
- In Silico Laboratory: New and Updated Tools for Protein-Centered Drug Discovery.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Cheminformatic analysis of protein surfaces provides binding site insights and informs identification strategies.Future medicinal chemistry · 2025Article
- Unveiling polyphenol-protein interactions: a comprehensive computational analysis.Journal of cheminformatics · 2025Article
- Identification of Furin Protease Small-Molecule Inhibitor with a 1,3-Thiazol-2-ylaminosulfonyl Scaffold.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Article
- Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach.Journal of chemical information and modeling · 2023Article
- Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.Journal of chemical information and modeling · 2022Article
- Boosting the Full Potential of PyMOL with Structural Biology Plugins.Biomolecules · 2022Review
- Quantum Chemical Microsolvation by Automated Water Placement.Molecules (Basel, Switzerland) · 2021Article
- Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case.The journal of physical chemistry letters · 2021Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ProBiS H2O MD approach for identification of conserved waters and water sites of interest in macromolecular systems, which is becoming a typical step in a structure-based drug design or macromolecular study in general, is described. This work explores an extension of the ProBiS H2O approach introduced by Jukič et al. Indeed, water molecules are key players in the interaction mechanisms of macromolecules and small molecules and play structural roles. Our earlier developed approach, ProBiS H2O, is a simple and transparent workflow for conserved water detection. Here we have considered generalizing the idea by supplementing the experimental data with data derived from molecular dynamics to facilitate work on less known systems. Newly developed ProBiS H2O MD workflow uses trajectory data, extracts and identifies interesting water sites, and visualizes the results. ProBiS H2O MD can thus robustly process molecular dynamic trajectory snapshots, perform local superpositions, collect water location data, and perform density-based clustering to identify discrete sites with high conservation of water molecules. This is a new approach that uses experimental data
Identifiers
What OpenQuestion holds
Registered trials
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