A hierarchical, two-stage approach to ab initio protein structure prediction is presented and
applied to four α-helical proteins. In the first stage, a bank of low-resolution models is …

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and
we apply the method to proteins. Using a small number of coarse-grained sites (about one …

INFORMATION TO USERS Page 1 INFORMATION TO USERS The negative microfilm of
this dissertation was prepared and inspected by the school granting the degree. We are …

Highlights of the evolutionary development of the physical approach to biology during the
last 80 years are traced in this chapter. The historical sequence of events that led to the …

Understanding protein–protein recognition is one of the main goals in structural biology.
Most of the key biological processes involve the formation of specific protein complexes, for …

Using the harmonic-approximation approach of the accompanying paper and AM1 energy
surfaces of terminally-blocked amino-acid residues, we determined physics-based side …

Molecular simulation models have provided immense, often general, insight into the
complex behavior of protein systems. Even for very detailed, eg, atomistic, models, the …

This chapter summarizes the theoretical principles of the construction of physics-based
coarse-grained force fields. It describes the UNited-RESidue (UNRES) force field, together …

Homology modeling is integral to structure-based drug discovery. Robust homology
modeling to atomic-level accuracy requires in the general case successful prediction of …