Analysis of the literature involving computational modeling of diseases and drug design with
the aid of experimental spectroscopic techniques reveals that this specific combination of …

Background Structure-based computational methods are needed to help identify and
characterize protein-protein complexes and their function. For individual proteins, the most …

Computational protein design depends on an energy function and an algorithm to search
the sequence/conformation space. We compare three stochastic search algorithms: a …

PDZ domains direct protein–protein interactions and serve as models for protein design.
Here, we optimized a protein design energy function for the Tiam1 and Cask PDZ domains …

Computationally designed protein sequences have been proposed as a basis to perform
fold recognition and homology searching. To investigate this possibility, an automated …

What are the key building blocks that would have been needed to construct complex protein
folds? This is an important issue for understanding protein folding mechanism and guiding …

Reduced amino acid alphabets are useful to understand molecular evolution as they reveal
basal, shared properties of amino acids, which the structures and functions of proteins rely …

Background Protein fold recognition usually relies on a statistical model of each fold; each
model is constructed from an ensemble of natural sequences belonging to that fold. A …

In the era of structural genomics, the prediction of protein interactions using docking
algorithms is an important goal. The success of this method critically relies on the …

The full information required to fold a protein is contained in its amino acid sequence. The
folding is governed by local sequence/structure propensity and also by long-range …