Proteins are dynamic entities whose conformations change in response to external stimuli [1]. Many experimental studies have demonstrated that protein exibility is crucial for functioning [2-4], and clear evidence exists that evolution has made an e ort to rene not only the structures, but also the exibility pattern of proteins [5-14]. An analysis of structural databases outlines many examples of proteins displaying structural polymorphism [8,12-15]; that

Dynamic Nature of Proteins 339 Basic dMD Algorithm 341 dMD Force Fields 343 Implementation of dMD 347

dMD in Web Servers 350 Application of dMD in Biomolecular Problems 350

Protein Folding 350 Protein Structural Renement and Design 351 RNA Structural Predictions 351 Protein Aggregation 352 Equilibrium Protein Dynamics 352 Conformational Transitions 353 Protein-Protein Docking 353

Conclusions 355 References 355

is, cases where, depending on the crystallization conditions or the presence of e ectors, the same protein is found in two di erent conformations (in some cases, separated by more than 20 Å in root-mean-square deviation (RMSD) [16]). Undoubtedly, as structural techniques advance, more examples of dramatic conformational changes in proteins will emerge, showing the magnitude of the biological impact of protein exibility [12,13].