Paper Citing NAMD - Abstract
Kass, Itamar; Reboul, Cyril F.; Buckle, Ashley M.
COMPUTATIONAL METHODS FOR STUDYING SERPIN CONFORMATIONAL CHANGE AND STRUCTURAL PLASTICITY
METHODS IN ENZYMOLOGY, VOL 501: SERPIN STRUCTURE AND EVOLUTION, 501:295-323, 2011
Currently, over a hundred high-resolution structures of serpins are available, exhibiting a wide range of conformations. However, our understanding of serpin dynamics and conformational change is still limited, mainly due to challenges of monitoring structural changes and characterizing transient conformations using experimental methods. Insight can be provided, however, by employing theoretical and computational approaches. In this chapter, we present an overview of such methods, focusing on molecular dynamics and simulation. As serpin conformational dynamics span a wide range of timescales, we discuss the relative merits of each method and suggest which method is suited to specific conformational phenomena.
