โ Scribed by Emiko Furuichi; Patrice Koehl
No coin nor oath required. For personal study only.
A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein threedimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 A ห). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing โฃ-proteins will only perform best on โฃ-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149,
๐ SIMILAR VOLUMES
In this work we apply the 2C-DFT (two-component density-functional theory) within the Kohn-Sham scheme and the local density approximation in the limit of small positron densities to the determination of the electron and positron states of one positron in the alkali metals lithium, sodium and potass
contains papers and commentary arising from the Third Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, more familiarly known as CASP3
## Abstract Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle Xโray scattering studies suggest random coil behavior, calling for a coherent understanding of these seemingly contradicting obse
With the objective of improving side-chain conformation prediction, we have analyzed the influence of various factors on prediction by the Self-Consistent Mean Field Theory method, applied to a set of high resolution x-ray protein structure models. These factors may be classed as variations in the m
## Abstract The dielectric properties of the polar solvent on the proteinโsolvent interface at small intercharge distances are still poorly explored. To deconvolute this problem and to evaluate the pairโwise electrostatic interaction (PEI) energies of the point charges located at the proteinโsolven