Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha, beta, and alpha/beta structural classes

Article Abstract:

Three energy functions were developed to simulate the free energy of proteins from the alpha, beta and alpha/beta structural classes is presented. The study finally uses a simple model system to show that the VMC protocol does not require exhaustive sampling of medium- and high-energy structures in order to optimize the parameters of the potential energy adequately.

Atomic properties

---

Prediction of residue-residue pair frequencies in proteins.

Article Abstract:

The residue-residue pair frequencies widely used in threading and in simulating protein folding can be reproduced by a simple physical model is shown. The radical-distance based model, constructed and tested on a set of 243 nonhomologous proteins with a clear physical basis holds important clues for structure prediction is proposed.

---

Salt bridges stabilize the folded structure of barnase

Article Abstract:

The role of three Arg-Asp salt bridges in barnase is studied by extensive continuum-electrostatic calculations. The three salt bridges stabilize the structure of the barnase because the electrostatic involving the ionic partners overcomes the desolvating costs.

Usage, Observations, Electric properties, Electrostatics, Ions

Similar abstracts:

• Abstracts: Range and energy of interaction at infinite dilution in aqueous solutions of alcohols and hydrocarbons. On density microheterogeneities in dilute supercritical solutions
• Abstracts: Weak intermolecular interactions and molecular recognition: structure and dynamics of the benzene and pyridine p-tert-butylcalix[4]arene inclusions
• Abstracts: Driving force dependence of photoinduced electron transfer dynamics of intercalated molecules in DNA. Distance dependence of electron transfer in DNA: the role of the reorganization energy and free energy
• Abstracts: Isotope-based discrimination between the infrared modes of plastosemiquinone anion radicals and neutral tyrosyl radicals in photosystem II
• Abstracts: Theoretical study of binding of hydrated Zn(II) and Mg(II) cations to 5'-guanosine monophosphate. Toward polarizable molecular mechanics for DNA and RNA

This website is not affiliated with document authors or copyright owners. This page is provided for informational purposes only. Unintentional errors are possible.