HPHOB

An online tool to compute FOD model parameters for selected protein structures

Based on a computational module developed by Irena Roterman and Leszek Konieczny, and implemented by Katarzyna Stąpor and Piotr Fabian.

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The HPHOB application computes the degree to which the given protein molecule complies with the micelle-like structural pattern, mathematically modeled as a 3D Gaussian distribution of hydrophobicity. In this model, participation of the aqueous solvent directs hydrophobic residues towards the central part of the protein body, while exposure of polar residues on the surface makes the protein soluble. Local deviations from the model - such as exposure of hydrophobicity on the surface - prime the protein for interaction with selected molecules (ligands or substrates), which is why actual proteins do not follow the micelle-like structure with perfect accuracy.

The Relative Distance (RD) parameter mathematically expresses the difference between the actual (observed) structure of the target protein, and its corresponding mathematical model. Values below 0.5 indicate the presence of a well-defined hydrophobic core, overlaid by a hydrophilic shell, while higher values suggest that no such core is present.

To calculate RD values for the target protein, please begin by entering its Protein DataBank (PDB) identifier. You will then be prompted to select specific secondary folds or residue ranges (up to the entire PDB structure) for analysis.

If you publish results obtained at least partially by using this service, please include the following citations in your publication:

  • Kalinowska B, Banach M, Konieczny L, Roterman I, "Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins"; Entropy 2015, 17(3), 1477-1507; https://doi.org/10.3390/e17031477
  • Roterman-Konieczna I, "From globular proteins to amyloids”; Amsterdam, The Netherlands; Oxford, UK; Cambridge MA. USA; Elsevier 2020
  • Konieczny L, Roterman I, "Description of the fuzzy oil drop model", in: Roterman-Konieczna I, ed., From Globular Proteins to Amyloids, pp. 1-12, Elsevier 2020, Amsterdam, The Netherlands; Oxford, UK; Cambridge MA, USA; Electronic version available : https://www.sciencedirect.com/book/9780081029817/from-globular-proteins-to-amyloids
Please supply a 4-character code of a protein. Pressing the Search button will look for that protein inside RCSB's Protein Data Bank (PDB). If the protein is found, it will be downloaded and presented for your inspection before further processing.