Loading...

Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions

Radja, N.H ; Sharif University of Technology | 2005

274 Viewed
  1. Type of Document: Article
  2. DOI: 10.1103/PhysRevE.72.061915
  3. Publisher: 2005
  4. Abstract:
  5. We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of designability ranking shows that about 1/e of the structures have designabilities above the average, independent on the used model. © 2005 The American Physical Society
  6. Keywords:
  7. Additives ; Hydrophilicity ; Mathematical models ; Proteins ; Structural design ; Vectors ; Interactions ; Miyazawa-Jernigan interactions ; Solvation ; Contacts (fluid mechanics) ; Amino acid ; Protein ; Protein binding ; Solvent ; Binding site ; Chemical model ; Chemical structure ; Chemistry ; Computer simulation ; Protein conformation ; Statistical model ; Amino Acids ; Binding Sites ; Models, Chemical ; Models, Molecular ; Models, Statistical ; Solvents
  8. Source: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 72, Issue 6 , 2005 ; 15393755 (ISSN)
  9. URL: https://journals.aps.org/pre/abstract/10.1103/PhysRevE.72.061915