Computational protein design with explicit consideration of surface hydrophobic patches

Free Form Surface Design with A-Patches·

We present a sufficient criterion for the Bernstein-Bezier (BB) form of a trivariate polynomial within a tetrahedron, such that the real zero contour of the polynomial defines a smooth and single sheeted algebraic surface patch. We call this an A-patch. We present algorithms to build a mesh of cubic A-patches to interpolate a given set of scattered point data in three dimensions, respecting the...

Compact Representation of Protein Surface Patches

Introduction Prediction of protein structure from amino acid (AA) sequence is one of the grand challenges of modern biochemistry. While ab initio structure prediction is difficult, prediction of local structure is more tractable if experimentally determined structures of homologous proteins exist. The prediction of local patches is useful in predicting interaction partners of proteins and nucle...

Solvent structure at a hydrophobic protein surface.

The impact of an extensive, uniform and hydrophobic protein surface on the behavior of the surrounding solvent is investigated. In particular, focus is placed on the possible enhancement of the structure of water at the interface, one model for the hydrophobic effect. Solvent residence times and radial distribution functions are analyzed around three types of atomic sites (methyl, polar, and po...

Fault Tolerant Control System Design with Explicit Consideration of Performance Degradation

To design fault tolerant control systems (FTCS), one of the important issues to consider is whether to recover the original system performance/functionality completely or to accept some degree of performance degradation after occurrence of a fault. What are the consequences if the performance degradation is not taken into consideration and how to take such performance degradation into account i...

A new library of surface patches - design and applications