NEPRE: a Scoring Function for Protein Structures based on Neighbourhood Preference

Abstract

Protein structure prediction relies on two major components, a method to generate good models that are close to the native structure and a scoring function that can select the good models. Based on the statistics from known structures in the protein data bank, a statistical energy function is derived to reflect the amino acid neighbourhood preferences. The neighbourhood of one amino acid is defined by its contacting residues, and the energy function is determined by the neighbhoring residue types and relative positions. A scoring algorithm, Nepre, has been implemented and its performance was tested with several decoy sets. The results show that the Nepre program can be applied in model ranking to improve the success rate in structure predictions.

Water‐based Supercapacitors with Amino Acid Electrolytes: A Green Perspective for Capacitance Enhancement

“…At higher specific currents (e. g., > 2-3 A/g), the excessive viscosity of amino acid-based electrolytes (up to ~40 cP for 10 m Lys, Figure 2b) [42] limits the rate capability of the EDLCs. In addition, the size of amino acid molecules (~0.36-0.5 nm [43] ) is larger than the nitrate salt ions (0.3-0.35 [44] ), which may instead easily access the micropores of the active materials, whose pore size distribution is shown in Figure S3. The non-straight shape of the GCD obtained with 10 m Lys is also a sign of ion diffusion limitations.…”

“…In [44] , the hydrated ionic radius is rated 3.58 Å for Na + and 3.35 Å for NO 3 À , while the radii for L-proline and L-lysine the respective radii are 3.61 Å and 5.02 Å, respectively, based on the analysis of contacting residues in existing proteins. [43] A range of 2.5-3.5 Å is assumed for the Helmholtz layer of pure 2 M NaNO 3 electrolyte while a slightly higher range 3-5 Å is expected in the presence of 10 m L-proline due to the larger size of the amino acid molecule; lastly, a conservative range 6-8 Å is assumed for 10 m L-lysine, since in this case the ion size of charged L-lysine + and L-lysine À is bigger than Na + and NO 3 À . In the simplified framework of the above model, it is possible to show that amino acid addition to the water:salt electrolyte dramatically improves the e r of the electrolyte, increasing the surface capacitance of the HOPG/electrolyte interface (Figure 5).…”