▪ Abstract Comparative modeling predicts the three-dimensional structure of a given protein
sequence (target) based primarily on its alignment to one or more proteins of known …

During the process of protein folding, the amino acid residues along the polypeptide chain
interact with each other in a cooperative manner to form the stable native structure. The …

We explore the ability of a simple simulated annealing procedure to assemble native-like
structures from fragments of unrelated protein structures with similar local sequences using …

A new protein fold recognition method is described which is both fast and reliable. The
method uses a traditional sequence alignment algorithm to generate alignments which are …

We present a formalism to compute the probability of an amino acid sequence conformation
being native-like, given a set of pairwise atom-atom distances. The formalism is used to …

Determination of the three dimensional (3D) structure of a protein can provide important
details about its biological functions and mechanism of action. However, despite their …

A useful three-dimensional (3D) model for a protein of unknown structure (the target) can
frequently be built based on one or more related proteins of known structure (the templates) …

In fold recognition by threading one takes the amino acid sequence of a protein and
evaluates how well it fits into one of the known three-dimensional (3D) protein structures …

Knowing the coordination number and relative solvent accessibility of all the residues in a
protein is crucial for deriving constraints useful in modeling protein folding and protein …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …