Biokinematic protein simulation by an adaptive dihedral angle approach

• High computational cost makes protein motion simulation a difficult problem.
• Presented procedure obtains protein motion without using energy minimization.
• Results are obtained for four proteins of different size and movement type.
• A preliminary study for folding paths study is presented.

Protein motion simulation is still a troublesome problem yet to be solved, especially due to its high computational requirements. Accurate methodologies such as molecular dynamics have too much computational cost in order to simulate protein motion. On the other hand, less accurate procedures, such as interpolation methods, do not obtain realistic paths but mere estimations, usually resulting in kinematically impossible paths. The procedure presented in this paper tries to merge both approaches as it obtains protein motion by adaptive dihedral angle increment application, without making use of energy minimization processes. The presented procedure is an evolution of our previous works, as it provides the protein with more movement capacities, being able to search a wider configurational space. Also, structures are normalized in order to minimize inaccuracies introduced by experimental methods, providing a more efficient but still accurate structure for motion simulation.