Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Ab initio Protein Structure Prediction
Conformational Search Methods
Molecular Dynamics

When calculating MD (which is discussed in detail in Chapter 10), Newton's equations of motion are solved at each step of atomic movement. This is arguably the most reliable method for describing protein processes at the atomic level. Consequently, it is more frequently used than other Methods to study protein Folding Pathways (Duan and Kollman 1998). Long computation times represent one of the primary challenges of this method, as the time step is typically on the order of femtoseconds (10^-15 s), whereas the fastest natural folding time for a small protein (fewer than 100 residues) falls in the millisecond range. To date, no serious attempts have been made to perform all-atom MD calculations for Structure/41.html">Cell/13.html">Protein Structure Prediction starting from an extended or disordered structure⁵. When a low-resolution model is available, MD calculations are frequently employed for structure refinement, assuming that conformational changes will be minor. Worthy of note is the approach used in recent work by Scheraga and colleagues, who implemented MD calculations in torsional angle space using the UNRES coarse-grained energy potential (see Discussion above).