Abstract
Flexibility in biomolecules is an important determinant of biological functionality. Almost all enzymatic and chemical reactions involve a significant conformational change of the protein and, in general, of the associated ligand.
The motions that lead to these conformational changes can be large and occur on time scales that are long compared with thermal vibrations; standard molecular dynamics must therefore be augmented by new approaches.
This workshop (http:// biophysics.asu.edu/workshop_2005/index.html) was held in Tempe, Arizona, USA from 15–18 May 2005, and brought together biochemists, chemists, computer scientists, mathematicians and physicists, in an effort to identify and promote the most promising approaches for studying flexibility in biomolecules and biomolecular complexes.
The 12 papers that are published in this volume represent a good cross section of the work presented at the workshop. The first papers focus on understanding the structure of the energy landscape of small proteins using full-atom description and various methods allowing a faster sampling of the phase space. The second series of papers focuses more directly on flexibility of biomolecules using topological tools. The third group of papers uses simplified representations in order to address flexibility on a large scale involving thousands of residues.
This collection sets out what we think are some of the more promising theoretical approaches currently being explored to study flexibility in biomolecules. We believe that they will be useful to anybody interested in studying this fascinating problem, that is likely to remain challenging for many years to come.