Since its introduction, the basin hopping (BH) framework has proven useful for hard
nonlinear optimization problems with multiple variables and modalities. Applications span a …

Ab-initio structure prediction refers to the problem of using only knowledge of the sequence
of amino acids in a protein molecule to find spatial arrangements, or conformations, of the …

Adequate sampling of the conformational space is a central challenge in ab initio protein
structure prediction. In the absence of a template structure, a conformational search …

Background Many proteins tune their biological function by transitioning between different
functional states, effectively acting as dynamic molecular machines. Detailed structural …

Background Whenever suitable template structures are not available, usage of fragment-
based protein structure prediction becomes the only practical alternative as pure ab initio …

Background Elucidating the native structure of a protein molecule from its sequence of
amino acids, a problem known as de novo structure prediction, is a long standing challenge …

More than fifty years of research in molecular biology have demonstrated that the ability of
small and large molecules to interact with one another and propagate the cellular processes …

The User Requirements Notation is a standard published by the International
Telecommunication Union that contains two complementary notations for goal and …

Protein structure prediction is considered a main challenge in computational biology. The
biannual international competition, Critical Assessment of protein Structure Prediction …

Sampling-based motion planning algorithms from the field of robotics have been very
successful in exploring the conformational space of proteins. However, studying the …