Molecular Modeling Of Proteins And Mathematical Prediction Of Protein Structure.pdf

MOLECULARMODELINGOFPROTEINSANDMATHEMATICALPREDICTIONOFPROTEINSTRUCTUREARNOLDNEUMAIER?-(native,tertiary)structureofaprotein,,,thereareseveralmainsidestothestaticproblem:–theselectionofanappropriatepotentialenergyfunction;–theparameteridenti?cationby?ttingtoexperimentaldata;and–,inaddition,thesolutionof(becauseofmultipletimescalesverysti?)ordinaryorstochasticdi?erentialequations(moleculardynamicssimulation),or(incaseofconstrainedmoleculardynamics)ofdi?erential--,somede?cienciesofthecurrentmodelsandalgorithms,andpossible(pastandfuture),molecularmechanics,transitionstates,stochasticdi?erentialequations,dynamicenergyminimization,harmonicapproximation,multipletimescales,sti?ness,di?erential-algebraicequation,moleculardynamicssimulations,potentialenergysurface,parameterestimation,conformationalentropy,secondarystructure,tertiarystructure,nativestructure,confor-mationalentropy,globaloptimization,simulatedannealing,icalgorithm,smoothingmethod,di?usionequationmethod,branchandbound,backbonepotentialmodels,latticemodels,contactpotential,threading,binationruleAMSsubjectclassi?;secondary65L05,’sprivilegetoconcealthings,butthekings’prideistoresearchthem.(Proverbs25:2;ascribedtoKingSolomonofIsrael,c