Empirical force fields for biological macromolecules: Overview and issues

@article{MacKerell2004EmpiricalFF,
  title={Empirical force fields for biological macromolecules: Overview and issues},
  author={Alexander D. MacKerell},
  journal={Journal of Computational Chemistry},
  year={2004},
  volume={25}
}
Empirical force field‐based studies of biological macromolecules are becoming a common tool for investigating their structure–activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field‐based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate… 

Polarizable force fields for molecular dynamics simulations of biomolecules

Molecular dynamics simulations are well established for the study of biomolecular systems. Within these simulations, energy functions known as force fields are used to determine the forces acting on

Recent developments and applications of the CHARMM force fields

The objective of the present review is to provide an up‐to‐date overview of the CHARMM FFs, including underlying methodologies and principles, along with a brief description of the strategies used for parameter development.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications

The commonly used methodologies for modeling electronic polarization are presented along with an overview of selected application studies, which include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods.

Comparison of protein force fields for molecular dynamics simulations.

This review describes the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA and their ability to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.

Force Fields for Small Molecules.

This chapter focuses on the development of small molecule force fields with emphasis on polarizable models, and the potential importance of polarization for their application in a wide range of biological systems including CADD.

Analytical electrostatics for biomolecules: beyond the generalized Born approximation.

A method based on an approximate analytical solution of the linearized Poisson-Boltzmann equation for a sphere is extended to biomolecules of arbitrary shape and provides computationally efficient algorithms for estimation of the parameters of the model.

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step toward an accurate

Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms

The accuracy of molecular mechanics force fields (FF) reveals critical for applications where precise molecular structures along a conformational sampling are required, as in the simulation of

AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA.

  • Lei HuangB. Roux
  • Chemistry, Physics
    Journal of chemical theory and computation
  • 2013
This work proposes a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data.
...

References

SHOWING 1-10 OF 541 REFERENCES

All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

Empirical force‐field calculations on biological molecules represent an effective method to obtain atomic detail information on the relationship of their structure to their function. Results from

Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise *

An overview of the experiences, some cautionary notes, and recommendations for further study in molecular dynamics simulation of nucleic acids are provided.

Force fields for protein simulations.

Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests

The results show that, although the overall accuracy is no better than what can be achieved with a fixed‐charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields.

Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

The relationship between DNA structure and function is fundamental to the understanding of biological processes. Currently, the most reliable source of biomolecular structural information comes from

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

Structural behavior during molecular dynamics with the modified force field is found to be very similar to expectations, suggesting that these basis sets of conformations may themselves have significant transferability among force fields.

Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

To improve the treatment of the peptide backbone, quantum mechanical and molecular mechanical calculations were undertaken on the alanine, glycine, and proline dipeptides, and the results were combined with molecular dynamics simulations of proteins in crystal and aqueous environments to enhance the quality of the CHARMM force field.

Polarizable force fields.

Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution

The objective of this work is to obtain a water model for simulations of biological macromolecules in solution. A pragmatic approach is taken in which we use the same type of force field for the

Development and current status of the CHARMM force field for nucleic acids

The CHARMM27 all‐atom force field for nucleic acids represents a highly optimized model for investigations ofucleic acids via empirical force field calculations, compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems.
...