A perspective on sustainable computational chemistry software development and integration

R Di Felice, ML Mayes, RM Richard… - Journal of chemical …, 2023 - ACS Publications
The power of quantum chemistry to predict the ground and excited state properties of
complex chemical systems has driven the development of computational quantum chemistry …

Genome editing in cotton: challenges and opportunities

Z Khan, SH Khan, A Ahmed, MU Iqbal… - Journal of Cotton …, 2023 - Springer
Cotton has enormous economic potential providing high-quality protein, oil, and fibre. A
large increase in cotton output is necessary due to the world's changing climate and …

Machines on genes through the computational microscope

S Sinha, C Pindi, M Ahsan, PR Arantes… - Journal of chemical …, 2023 - ACS Publications
Macromolecular machines acting on genes are at the core of life's fundamental processes,
including DNA replication and repair, gene transcription and regulation, chromatin …

Cas12a domain flexibility guides R-loop formation and forces RuvC resetting

I Strohkendl, A Saha, C Moy, AH Nguyen, M Ahsan… - Molecular Cell, 2024 - cell.com
The specific nature of CRISPR-Cas12a makes it a desirable RNA-guided endonuclease for
biotechnology and therapeutic applications. To understand how R-loop formation within the …

An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a

A Saha, M Ahsan, PR Arantes, M Schmitz… - Nature …, 2024 - nature.com
CRISPR-Cas12a is a powerful RNA-guided genome-editing system that generates double-
strand DNA breaks using its single RuvC nuclease domain by a sequential mechanism in …

The electronic structure of genome editors from the first principles

Ł Nierzwicki, M Ahsan, G Palermo - Electronic Structure, 2023 - iopscience.iop.org
Ab-initio molecular dynamics enables following the dynamics of biological systems from the
first principles, describing the electronic structure and offering the opportunity to" watch" the …

Constructing next-generation CRISPR–Cas tools from structural blueprints

JPK Bravo, GN Hibshman, DW Taylor - Current Opinion in Biotechnology, 2022 - Elsevier
Highlights•Target binding and R-loop formation by Cas9 require conformational
rearrangements.•Structural insights enable the development of efficient and high-fidelity …

Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering

KT Korbeld, MJLJ Fürst - ChemBioChem, 2023 - Wiley Online Library
Enzyme engineering aims to improve or install a new function in biocatalysts for applications
ranging from chemical synthesis to biomedicine. For decades, computational techniques …

Structure of Geobacillus stearothermophilus Cas9: Insights into the Catalytic Process and Thermostability of CRISPR-Cas9

P Shen, L Zhang, B Liu, X Li, C Wang, J Min… - ACS …, 2024 - ACS Publications
CRISPR-Cas9 has been developed as a powerful gene editing tool, but the mechanism that
governs its intricate catalytic process remains incompletely resolved. Here, the cryo-electron …

Exploring CRISPR-Cas9 HNH-Domain-Catalyzed DNA Cleavage Using Accelerated Quantum Mechanical Molecular Mechanical Free Energy Simulation

R Van, X Pan, S Rostami, J Liu, PK Agarwal… - Biochemistry, 2024 - ACS Publications
The target DNA (tDNA) cleavage catalyzed by the CRISPR Cas9 enzyme is a critical step in
the Cas9-based genome editing technologies. Previously, the tDNA cleavage from an active …