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

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

Continuous evolution of base editors with expanded target compatibility and improved activity

(2019) Benjamin W. Thuronyi et al.   NATURE BIOTECHNOLOGY

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

(2019) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

Continuous directed evolution of proteins with improved soluble expression

(2018) Tina Wang et al.   Nature Chemical Biology

Base editing: precision chemistry on the genome and transcriptome of living cells

(2018) Holly A. Rees et al.   NATURE REVIEWS GENETICS

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

(2017) Nicole M. Gaudelli et al.   NATURE

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Structural insights into DNA cleavage activation of CRISPR-Cas9 system

(2017) Cong Huai et al.   Nature Communications

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B

(2017) Ke Shi et al.   Scientific Reports

Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance

(2016) Ahmed H. Badran et al.   NATURE

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

(2016) Alexis C. Komor et al.   NATURE

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

(2016) F. Jiang et al.   SCIENCE

The APOBEC Protein Family: United by Structure, Divergent in Function

(2016) Jason D. Salter et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

(2016) Ke Shi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer 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

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

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

Optimizing non-natural protein function with directed evolution

(2010) Eric M Brustad et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications

(2008) Lauren G. Holden et al.   NATURE

The AID/APOBEC family of nucleic acid mutators

(2008) Silvestro G Conticello   GENOME BIOLOGY