4.7 Article

Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Chemistry, Physical

Stress tensor and constant pressure simulation for polarizable Gaussian multipole model

Haixin Wei et al.

Summary: In this article, we establish the theory of molecular dynamics (MD) simulations with the polarizable Gaussian multipole (pGM) electrostatics, and derive the pGM internal stress tensor for constant pressure MD simulations. We present different formulations for flexible, rigid, and short-range screened systems. The analytical formulations are implemented and validated, and differences between pGM and classic point charge models are observed.

JOURNAL OF CHEMICAL PHYSICS (2022)

Article Chemistry, Physical

PyRESP: A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields

Shiji Zhao et al.

Summary: Molecular modeling at the atomic level is widely used in biological systems. However, additive force fields that rely on fixed atom-centered partial charges cannot accurately simulate polarization effects. This study presents PyRESP, a Python program that parameterizes atomic multipole moments by reproducing the ab initio electrostatic potential around molecules, catering to the needs of force field parameterizations in molecular modeling.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2022)

Article Chemistry, Medicinal

Development of a Pantetheine Force Field Library for Molecular Modeling

Shiji Zhao et al.

Summary: The development of the Pantetheine Force Field (PFF) library allows for the modeling of systems containing PCLs in silico, supporting various applications including protein engineering and drug discovery. Validation studies have shown promising performance in molecular dynamics simulations compared to experimental data of representative systems.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

Article Chemistry, Physical

Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations

Edward King et al.

Summary: Accurate prediction of binding free energies is crucial for drug development and protein design. Absolute alchemical methods provide a rigorous approach that considers flexibility and solvent interaction. The importance of electronic polarization in binding affinity prediction has been demonstrated through extensive simulations.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Chemistry, Physical

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)

Article Chemistry, Physical

Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations

Haixin Wei et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Biochemistry & Molecular Biology

Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM*

Robert E. Duke et al.

JOURNAL OF MOLECULAR MODELING (2019)

Article Chemistry, Medicinal

GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features

Tai-Sung Lee et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)

Article Chemistry, Physical

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

Karl T. Debiec et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2016)

Review Biochemistry & Molecular Biology

Understanding Nucleic Acid-Ion Interactions

Jan Lipfert et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 83 (2014)

Article Chemistry, Physical

Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches

Amanda Li et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Computer Science, Interdisciplinary Applications

SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations

Scott Le Grand et al.

COMPUTER PHYSICS COMMUNICATIONS (2013)

Article Chemistry, Physical

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

Yue Shi et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Chemistry, Physical

Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization

Junmei Wang et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

Article Chemistry, Physical

Gaussian Multipole Model (GMM)

Dennis M. Elking et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)

Article Chemistry, Multidisciplinary

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

Dennis M. Elking et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)

Article Biochemistry & Molecular Biology

Principles of protein folding - A perspective from simple exact models

Ken A. Dill et al.

PROTEIN SCIENCE (2010)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Review Physics, Condensed Matter

Polarization effects in molecular mechanical force fields

Piotr Cieplak et al.

JOURNAL OF PHYSICS-CONDENSED MATTER (2009)

Article Chemistry, Physical

Continuum polarizable force field within the Poisson-Boltzmann framework

Yu-Hong Tan et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Chemistry, Physical

Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections

Jeng-Da Chai et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2008)

Article Chemistry, Multidisciplinary

Gaussian induced dipole polarization model

Dennis Elking et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2007)

Review Chemistry, Physical

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator

Pedro E. M. Lopes et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2007)

Article Chemistry, Physical

Continuum treatment of electronic polarization effect

Yu-Hong Tan et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Chemistry, Physical

A polarizable model of water for molecular dynamics simulations of biomolecules

G Lamoureux et al.

CHEMICAL PHYSICS LETTERS (2006)

Article Chemistry, Multidisciplinary

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

S Patel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Review Chemistry, Physical

Polarizable atomic multipole water model for molecular mechanics simulation

PY Ren et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2003)

Article Chemistry, Multidisciplinary

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

PY Ren et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)