Publication

Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

Related publications (40)

Stimulus-responsive assembly of nonviral nucleocapsids

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

Nature Portfolio2024

RNA-based nanomedicines and their clinical applications

Yi Wang

RNA-based nanomedicines encompass a range of therapeutic approaches that utilize RNA molecules or molecules that target RNAs for the treatment or prevention of diseases. These include antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), endo ...

Beijing2023

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

Impact of Anion Asymmetry on Local Structure and Supercooling Behavior of Water-in-Salt Electrolytes

Corsin Battaglia, David Reber

Salts with asymmetric (fluorosulfonyl)(trifluoromethanesulfonyl)imide (FTFSI) anions have recently been shown to suppress crystallization of water-in-salt electrolytes, enabling low-temperature operation of high-voltage aqueous rechargeable batteries. To c ...

AMER CHEMICAL SOC2020

The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution

Benjamin Marcel Daniel Rothé

Non-coding RNAs associate with proteins to form ribonucleoproteins (RNPs), such as ribosome, box C/D snoRNPs, H/ACA snoRNPs, ribonuclease P, telomerase and spliceosome to ensure cell viability. The assembly of these RNA-protein complexes relies on the abil ...

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER2019

Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

Michele Ceriotti, Venkat Kapil

The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even th ...

American Institute of Physics2016

Principles of Systems Biology, No. 11

Vassily Hatzimanikatis, Jasmin Maria Hafner, Noushin Hadadi, Laurent Potvin-Trottier

This month: AI that learns patterns and facts, new protein-RNA and protein-protein relationships, engineering signaling and metabolism, and more variants of Cas9. ...

Cell Press2016

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

Matteo Dal Peraro, Andrea Cavalli, Giulia Palermo

Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, ...

Amer Chemical Soc2015

A Theoretical Rationalisation of the Emission Properties of Prototypical Cu(I)-Phenanthroline Complexes

Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold, Gloria Capano

The excited state properties of transition metal complexes have become a central focus of research owing to a wide range of possible applications that seek to exploit their luminescence properties. Herein, we use density functional theory (DFT), time-depen ...

2015

Detection of RNAP-DNA complexes using solid state nanopores

Aleksandra Radenovic, Michael Graf, Camille Alice Raillon

Transcription is the first step in gene expression where DNA is copied into RNA. It is extensively studied at the bulk level especially the regulation mechanism, which in cancerous cells is impaired. We were interested in studying E. coli RNAP enzyme at th ...

IEEE2013

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