ArticleFrontiers in molecular biosciences2021
Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network.
Article in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed, 55 citations in OpenAlex.
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- Exploring neural networks to uncover information-richer features for protein interaction prediction.European biophysics journal : EBJ · 2026Article
- Uncovering the molecular details of the 14-3-3 recruitment by mutant Sod1 species.Scientific reports · 2025Article
- Machine learning framework to extract physicochemical features of B-cell epitopes recognized by a cross-reactive antibody.NPJ systems biology and applications · 2025Article
- Introducing the PARCH Scale for Quantifying the Hydropathy of Nucleic Acids and Nucleic Acid-Protein Complexes.Langmuir : the ACS journal of surfaces and colloids · 2025Article
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale.The journal of physical chemistry. B · 2025Article
- Article
- Nanoscale Topography Dictates Residue Hydropathy in Proteins.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- High-Throughput Interactome Determination via Sulfur Anomalous Scattering.The journal of physical chemistry letters · 2024Article
- Impact of Excipient Extraction and Buffer Exchange on Recombinant Monoclonal Antibody Stability.Molecular pharmaceutics · 2024Article
- An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.Journal of chemical theory and computation · 2024Article
- Integrating machine learning to advance epitope mapping.Frontiers in immunology · 2024Review
- PepAnalyzer: predicting peptide properties using its sequence.Amino acids · 2023Article
- N-terminal alanine-rich (NTAR) sequences drive precise start codon selection resulting in elevated translation of multiple proteins including ERK1/2.Nucleic acids research · 2023Article
- Electrostatic complementarity at the interface drives transient protein-protein interactions.Scientific reports · 2023Article
- Caseins: Versatility of Their Micellar Organization in Relation to the Functional and Nutritional Properties of Milk.Molecules (Basel, Switzerland) · 2023Review
- Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex.Frontiers in molecular biosciences · 2023Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.
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