This module introduces the concept of free energy and potential fields in the context of protein conformation spaces and motion planning. It then provides examples of applications of motion planning techniques to problems from structural computational biology.

This study presents a site-resolved experimental view of backbone C &agr; H and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using 13C &agr; H and 15NH NMR relaxation data [ T 1 , T 2 , and NOE] acquired at three resonance frequencies (1H ...

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such ...

The paper addresses the seismic behavior of buildings with torsional eccentricies to a complex seismic wave environment. Specifically, the paper investigates the effects of nonsynchroneus seismic motion on a L-shaped building with significant torsional eccentricity. The building represents a typical concrete-steel composite industrial structure sitting on a soft soil deposit ...

The study of collective motions of molecules provides useful insights into the large amplitude conformational changes the molecules experiment during chemical reactions. In particular, theoretical normal modes analyses of proteins taking into account the lowestfrequency modes may help to predict the nature of such conformational changes. This work lists a ...

A normal modes analysis of the closed form of dimeric citrate synthase has been performed. The largest-amplitude collective motion predicted by this method compares well with the crystallographically observed hinge-bending motion. Such a result supports those obtained previously in the case of hinge-bending motions of smaller systems, such as lysozyme ...

Visiometric analysis of ratcheting is an application of computer visualization and animation to an experiment in combustion. In the experiment, a flame front is established over a circular porous plug burner at low pressure. As the flow rate is increased, the flame front exhibits a variety of spatial and temporal ...

The number of solved structures of macromolecules that have the same fold and thus exhibit some degree of conformational variability is rapidly increasing. It is consequently advantageous to develop a standardized terminology for describing this variability and automated systems for processing protein structures in different conformations. We have developed such ...

This study presents a site-resolved experimental view of backbone CαH and NH internal motions in the 56-residue immunoglobulin-binding domain of streptococcal protein G, GB1. Using 13CαH and 15NH NMR relaxation data [T1, T2, and NOE] acquired at three resonance frequencies (1H frequencies of 500, 600, and 800 MHz), spectral density ...