What is CUPSAT?

CUPSAT is a tool to predict changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. Additionally, the prediction model can distinguish the amino acid environment using its solvent accessibility and secondary structure specificity.


Key Features:

  • CUPSAT uses protein environment specific mean force potentials to predict protein stability.
  • Amino acid-atom potentials are used. For this, the 40 amino acid atom types from Melo-Feytmans are used to develop the radial pair distribution function.
  • Torsion angle potentials are derived from the distribution of main torsion angles φ and ψ.
  • Gaussian apodisation function has been used to accomodate torsion angle perturbation in protein mutants.
  • Mutant stability predictions from PDB as well as custom developed protein structures are possible.

References
  • Parthiban V, Gromiha MM and Schomburg D. (2006) CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Research, 34, W239-42. [PUBMED]
  • Vijaya Parthiban, M. Michael Gromiha, Christian Hoppe and Dietmar Schomburg. Structural Analysis and Prediction of Protein Mutant Stability using Distance and Torsion Potentials: Role of Secondary Structure and Solvent Accessibility. (2007) Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility. 66(1). 41-52. [PUBMED]
  • Parthiban, V., Gromiha, M. M., Abhinandan, M., Schomburg, D. (2007) Computational modeling of protein mutant stability: analysis and optimization of statistical potentials and structural features reveal insights into prediction model development. BMC Structural Biology. 7. 54. [PUBMED]