Detecting Native Protein Folds Among Large Decoy Sets with Hydrophobic Moment Profiling

Spatial profiling of protein hydrophobicity: native vs. decoy structures.

A recent study of 30 soluble globular protein structures revealed a quasi-invariant called the hydrophobic ratio. This invariant, which is the ratio of the distance at which the second order hydrophobic moment vanished to the distance at which the zero order moment vanished, was found to be 0.75 +/- 0.05 for 30 protein structures. This report first describes the results of the hydrophobic profi...

Detecting Native Protein Folds among Large Decoy Sets with the Opls All-atom Potential and the Surface Generalized Born Solvent Model

Recognizing native folds by the arrangement of hydrophobic and polar residues.

Central to the ab initio protein folding problem is the development of an energy function for which the correct native structure has a lower energy than all other conformations. Existing potentials of mean force typically rely extensively on database-derived contact frequencies or knowledge of three-dimensional structural information in order to be successful in the problem of recognizing the n...

Factors affecting the ability of energy functions to discriminate correct from incorrect folds.

Eighteen low and medium resolution empirical energy functions were tested for their ability to distinguish correct from incorrect folds from three test sets of decoy protein conformations. The energy functions included 13 pairwise potentials of mean force, covering a wide range of functional forms and methods of parameterization, four potentials that attempt to detect properly formed hydrophobi...

Atomically detailed potentials to recognize native and approximate protein structures.

Atomically detailed potentials for recognition of protein folds are presented. The potentials consist of pair interactions between atoms. One or three distance steps are used to describe the range of interactions between a pair. Training is carried out with the mathematical programming approach on the decoy sets of Baker, Levitt, and some of our own design. Recognition is required not only for ...