ArticleJournal of chemical theory and computation2024
An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Lipid-Shell PARCH: A Physically Motivated Scale for Transmembrane Residue Hydropathy.The journal of physical chemistry. B · 2026Article
- Context-Aware Hydrophobicity Modeling: HydroMap and FastHydroMap.bioRxiv : the preprint server for biology · 2026Article
- Hydropathy Landscapes of Histone-DNA Interactions in Chromatin Building Blocks.The journal of physical chemistry. B · 2026Article
- Decoding the Post-translational Modification Crosstalk: Functional Implications of Phosphorylation, Acetylation, and Methylation.The journal of physical chemistry. B · 2026Article
- Hydrophobicity in Intrinsically Disordered Protein Force Fields: Implications for Conformational Ensembles and Protein-Protein Interactions.The journal of physical chemistry. B · 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
- Extending the PARCH Scale: Assessing Hydropathy of Proteins across Multiple Water Models.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
- Tight junction regulation, intestinal permeability, and mucosal immunity in gastrointestinal health and disease.Current opinion in gastroenterology · 2025Review
- Nanoscale Topography Dictates Residue Hydropathy in Proteins.Langmuir : the ACS journal of surfaces and colloids · 2024Article
- Biophysics of claudin proteins in tight junction architecture: Three decades of progress.Biophysical journal · 2024Review
- Lipidation alters the phase-separation of resilin-like polypeptides.Soft matter · 2024Article
- The Role of ZO-2 in Modulating JAM-A and γ-Actin Junctional Recruitment, Apical Membrane and Tight Junction Tension, and Cell Response to Substrate Stiffness and Topography.International journal of molecular sciences · 2024Article
- Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels.Biomacromolecules · 2024Article
- Combined Computational-Biochemical Approach Offers an Accelerated Path to Membrane Protein Solubilization.Journal of chemical information and modeling · 2023Article
- Physico-Chemical Approaches to Investigate Surface Hydroxyls as Determinants of Molecular Initiating Events in Oxide Particle Toxicity.International journal of molecular sciences · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.