Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics-Reference-Cited by-同舟云学术

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics

Published:2017-04-19 Issue:5 Volume:13 Page:2053-2071
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Lemkul Justin A.¹^ORCID,MacKerell Alexander D.¹^ORCID

Affiliation:

1. Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States

Funder

Division of Graduate Education

National Institute of General Medical Sciences

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.7b00067

Reference87 articles.

1. Dynamics of folded proteins

2. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

3. A Modified Version of the Cornellet al.Force Field with Improved Sugar Pucker Phases and Helical Repeat

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

5. Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

Cited by 72 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. Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes;Journal of Chemical Theory and Computation;2024-07-16

2. Quantum Mechanics Characterization of Non-Covalent Interaction in Nucleotide Fragments;Molecules;2024-07-10

3. Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes;2024-05-07

4. Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction;Biophysical Journal;2024-05

5. sAMP‐VGG16: Force‐field assisted image‐based deep neural network prediction model for short antimicrobial peptides;Proteins: Structure, Function, and Bioinformatics;2024-03-23