Optimizations of protein force fields
Yoshitake Sakae, Yuko Okamoto
TL;DR
This paper reviews the development and optimization of force fields for protein molecular simulations, focusing on functional forms, parameter optimization methods, and comparative applications.
Contribution
It introduces new extensions to conventional force fields and discusses advanced parameter optimization techniques with practical application examples.
Findings
Optimized force fields improve simulation accuracy.
Extensions to functional forms enhance modeling capabilities.
Comparative analysis shows benefits over existing force fields.
Abstract
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventional ones. We then present various methods for force-field parameter optimizations. Finally, some examples of our applications of these parameter optimization methods are given and they are compared with the results from the existing force-fields.
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Taxonomy
TopicsProtein Structure and Dynamics · Protein purification and stability · Enzyme Structure and Function