RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
pluripotent chemical species in molecular biology, and its functions are intimately linked to …
Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications
Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional
theory by applying systematic approximations, leading to efficient computational schemes …
theory by applying systematic approximations, leading to efficient computational schemes …
Density-functional tight-binding: basic concepts and applications to molecules and clusters
F Spiegelman, N Tarrat, J Cuny, L Dontot… - … in physics: X, 2020 - Taylor & Francis
The scope of this article is to present an overview of the Density Functional based Tight
Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and …
Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and …
QDπ: A quantum deep potential interaction model for drug discovery
We report QDπ-v1. 0 for modeling the internal energy of drug molecules containing H, C, N,
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …
and O atoms. The QDπ model is in the form of a quantum mechanical/machine learning …
Stacking in RNA: NMR of four tetramers benchmark molecular dynamics
DE Condon, SD Kennedy, BC Mort… - Journal of chemical …, 2015 - ACS Publications
Molecular dynamics (MD) simulations for RNA tetramers r (AAAA), r (CAAU), r (GACC), and r
(UUUU) are benchmarked against 1H–1H NOESY distances and 3 J scalar couplings to test …
(UUUU) are benchmarked against 1H–1H NOESY distances and 3 J scalar couplings to test …
Development of range-corrected deep learning potentials for fast, accurate quantum mechanical/molecular mechanical simulations of chemical reactions in solution
We develop a new deep potential─ range correction (DPRc) machine learning potential for
combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical …
combined quantum mechanical/molecular mechanical (QM/MM) simulations of chemical …
Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase
Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced
selectivity and protection against overdosage. However, we need to better understand …
selectivity and protection against overdosage. However, we need to better understand …
Polarizable force field for DNA based on the classical Drude oscillator: I. Refinement using quantum mechanical base stacking and conformational energetics
JA Lemkul, AD MacKerell Jr - Journal of chemical theory and …, 2017 - ACS Publications
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus
yielding the forces governing its dynamics, using classical physics rather than more …
yielding the forces governing its dynamics, using classical physics rather than more …
Analyzing and biasing simulations with PLUMED
G Bussi, GA Tribello - Biomolecular Simulations: Methods and Protocols, 2019 - Springer
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to
analyze and bias molecular dynamics trajectories. The chapter begins by introducing the …
analyze and bias molecular dynamics trajectories. The chapter begins by introducing the …
On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules
RNA molecules play a vital role in biological processes within the cell, with significant
implications for science and medicine. Notably, the biological functions exerted by specific …
implications for science and medicine. Notably, the biological functions exerted by specific …