Editing Protein (section)

===In silico simulation of dynamical processes===

A more complex computational problem is the prediction of intermolecular interactions, such as in [[docking (molecular)|molecular docking]],<ref name=Ritchie2008/> [[protein folding]], [[protein–protein interaction]] and chemical reactivity. Mathematical models to simulate these dynamical processes involve [[molecular mechanics]], in particular, [[molecular dynamics]]. In this regard, ''[[in silico]]'' simulations discovered the folding of small α-helical [[protein domain]]s such as the [[villin]] headpiece,<ref name=Zagrovic2002/> the [[HIV]] accessory protein<ref name=Herges2005/> and hybrid methods combining standard molecular dynamics with [[quantum mechanics|quantum mechanical]] mathematics have explored the electronic states of [[rhodopsin]]s.<ref name=Hoffman2006/>

Beyond classical molecular dynamics, [[quantum dynamics]] methods allow the simulation of proteins in atomistic detail with an accurate description of quantum mechanical effects. Examples include the multi-layer [[multi-configuration time-dependent Hartree ]] method and the [[hierarchical equations of motion]] approach, which have been applied to plant cryptochromes<ref name= Gatti2018/> and bacteria light-harvesting complexes,<ref name= Schulten2012/> respectively. Both quantum and classical mechanical simulations of biological-scale systems are extremely computationally demanding, so [[distributed computing]] initiatives such as the [[Folding@home]] project facilitate the [[molecular modeling on GPU|molecular modeling]] by exploiting advances in [[Graphics processing unit|GPU]] parallel processing and [[Monte Carlo method|Monte Carlo]] techniques.<ref name=Scheraga2007/><ref name="Zheng Javidpour 2020">{{cite journal |last1=Zheng |first1=Size |last2=Javidpour |first2=Leili |last3=Sahimi |first3=Muhammad |last4=Shing |first4=Katherine S. |last5=Nakano |first5=Aiichiro |title=sDMD: An open source program for discontinuous molecular dynamics simulation of protein folding and aggregation |journal=Computer Physics Communications |volume=247 |date=2020 |doi=10.1016/j.cpc.2019.106873 |page=106873|bibcode=2020CoPhC.24706873Z }}</ref>