Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure-Reference-Cited by-同舟云学术

Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure

Published:2019 Issue:20 Volume:21 Page:10423-10435
ISSN:1463-9076
Container-title:Physical Chemistry Chemical Physics
language:en
Short-container-title:Phys. Chem. Chem. Phys.

Author:

Shao Qiang¹²³⁴⁵^ORCID,Yang Lijiang⁶⁷⁸⁹¹⁰,Zhu Weiliang¹²³⁴⁵

Affiliation:

1. Drug Discovery and Design Center

2. CAS Key Laboratory of Receptor Research

3. Shanghai Institute of Materia Medica

4. Chinese Academy of Sciences

5. Shanghai

6. Beijing National Laboratory for Molecular Sciences

7. Beijing

8. China

9. Institute of Theoretical and Computational Chemistry

10. College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center

Abstract

A dihedral-energy-based selective enhanced sampling method (D-SITSMD) is presented with improved capabilities for searching a protein's natively folded structure and for providing the underlying folding pathway.

Publisher

Royal Society of Chemistry (RSC)

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

Link

http://pubs.rsc.org/en/content/articlepdf/2019/CP/C9CP00615J

Reference65 articles.

1. Biomolecular Simulation: A Computational Microscope for Molecular Biology

2. Molecular dynamics simulations of biomolecules

3. Biomolecular Simulations: Recent Developments in Force Fields, Simulations of Enzyme Catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic Acid Noncovalent Interactions

4. Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

5. Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins

Cited by 6 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable;Protein Science;2024-01-23

2. Molecular Interactions and Forces that Make Proteins Stable: A Quantitative Inventory from Atomistic Molecular Dynamics Simulations;2023-01-23

3. The road less traveled in protein folding: evidence for multiple pathways;Current Opinion in Structural Biology;2021-02

4. Avoiding non-equilibrium effects in adaptive biasing force calculations;Molecular Simulation;2020-06-04

5. Exploring the Ligand Binding/Unbinding Pathway by Selectively Enhanced Sampling of Ligand in a Protein–Ligand Complex;The Journal of Physical Chemistry B;2019-09-03