Kavraki Lab

Physical and Biological Computing

Many large protein complexes undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. It is not always possible to obtain a high resolution structure for very large complexes. While many conformational search methods explore the motions of atomic resolution protein structures, little has been done to handle the abundance of coarser resolution data available. Traditional conformational search methods are impractical for very large complexes due to the amount of computational time involved.

Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE.  2009.  Tracing Conformational Changes in Proteins. IEEE Intl. Conf. on Bioinformatics and Biomedicine Workshops (BIBMW).

Haspel, N, Geisbrecht B, Lambris JD, Kavraki LE.  2009.  Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex. Proteins: Structure, function and bioinformatics. In press

Introduction

Proteins are flexible macromolecules, often changing shape/structure as needed to interact with other molecules. Structural fluctuations of proteins are related to their function. All the different structures that a protein assumes under physiological conditions contribute to its biological function.

Introduction

Protein motion plays a pivotal role in many biological studies that consider protein flexibility, such as drug discovery, protein folding, and other motion-related areas. When flexibility information is needed, researchers typically resort to the use of simulations (molecular dynamics, monte carlo, etc.) to sample protein conformations not seen in experimentally resolved structures, but that are physically possible.