相关论文: Optimization of protein force-field parameters wit…

We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…

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…

Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent…

Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…

We propose an automated protocol for designing the energy landscape of a protein energy function by optimizing its parameters. The parameters are optimized so that not only the global minimum energy conformation becomes native-like, but…

A central problem in biophysics and computational drug design is accurate modeling of biomolecules. The current molecular dynamics simulation methods can answer how a molecule inhibits a cancerous cell signaling pathway, or the role of…

Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural network that assigns all force field…

We apply the general protocol of parameter optimization (Lee, J. et al. Phys. Chem. B 2001, 105, 7291) to the UNRES potential. In contrast to the earlier works where only the relative weights of various interaction terms were optimized, we…

Protein characterization is one of the key components for understanding the human body and advancing drug discovery processes. While the future of quantum hardware holds the potential to accurately characterize these molecules, current…

This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…

Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…

Accurate force fields are necessary for predictive molecular simulations. However, developing force fields that accurately reproduce experimental properties is challenging. Here, we present a machine learning directed, multiobjective…

We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with…

Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or…

The applicability of the three steps systematic parametrization procedure (3SSPP) to develop a force field for primary amines was evaluated in the present work. Previous simulations of primary amines show that current force fields (FF) can…

An iterative optimization algorithm with MD simulations in the loop is developed and applied to optimize Lennard-Jones (LJ) parameters specific for liquid tri-n-butyl phosphate (TBP). The optimization loop uses non-dominated sorting genetic…

A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate in between these two methods, which can thus be interpreted…

The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…

We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…