Combined Theoretical, Bioinformatic, and Biochemical Analyses of RNA Editing by Adenine Base Editors

Insights into the Dual Shuttle Catalytic Mechanism of Guanine Deaminase

(2021) Asmita Sen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors

(2020) Kartik L. Rallapalli et al.   Science Advances

Directed evolution of adenine base editors with increased activity and therapeutic application

(2020) Nicole M. Gaudelli et al.   NATURE BIOTECHNOLOGY

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

(2020) Michelle F. Richter et al.   NATURE BIOTECHNOLOGY

Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity

(2020) Yi Yu et al.   Nature Communications

DNA capture by a CRISPR-Cas9–guided adenine base editor

(2020) Audrone Lapinaite et al.   SCIENCE

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

(2019) Erwei Zuo et al.   SCIENCE

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

(2019) Shuai Jin et al.   SCIENCE

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Adenine base editing in an adult mouse model of tyrosinaemia

(2019) Chun-Qing Song et al.   Nature Biomedical Engineering

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

(2019) Julian Grünewald et al.   NATURE

Analysis and minimization of cellular RNA editing by DNA adenine base editors

(2019) Holly A. Rees et al.   Science Advances

Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis

(2019) Changyang Zhou et al.   NATURE

Off-Target Editing by CRISPR-Guided DNA Base Editors

(2019) SeHee Park et al.   BIOCHEMISTRY

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

(2019) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Highly Efficient A·T to G·C Base Editing by Cas9n-Guided tRNA Adenosine Deaminase in Rice

(2018) Fang Yan et al.   Molecular Plant

Precise A·T to G·C Base Editing in the Rice Genome

(2018) Kai Hua et al.   Molecular Plant

Highly efficient RNA-guided base editing in rabbit

(2018) Zhiquan Liu et al.   Nature Communications

Correction of the Marfan Syndrome Pathogenic FBN1 Mutation by Base Editing in Human Cells and Heterozygous Embryos

(2018) Yanting Zeng et al.   MOLECULAR THERAPY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses

(2017) Adam Pecina et al.   Journal of Chemical Information and Modeling

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

MCPB.py: A Python Based Metal Center Parameter Builder

(2016) Pengfei Li et al.   Journal of Chemical Information and Modeling

Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD)

(2016) Xin Zhang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

Covariation Is a Poor Measure of Molecular Coevolution

(2015) David Talavera et al.   MOLECULAR BIOLOGY AND EVOLUTION

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Quantum mechanical/molecular mechanical studies of zinc hydrolases

(2014) Dingguo Xu et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study

(2014) Bianca Manta et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

(2014) Xiya Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

An overview of the Amber biomolecular simulation package

(2012) Romelia Salomon-Ferrer et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Simulations of Allosteric Motions in the Zinc Sensor CzrA

(2011) Dhruva K. Chakravorty et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

(2010) Pavel Banáš et al.   Journal of Chemical Theory and Computation

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY