Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks

YEATS Domains as Novel Epigenetic Readers: Structures, Functions, and Inhibitor Development

(2022) Xin Li et al.   ACS Chemical Biology

Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles

(2022) Masaki Kikuchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer

(2022) Lele Song et al.   MOLECULAR CELL

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

(2021) Ya Gao et al.   Journal of Chemical Information and Modeling

Histone Tail Conformations: A Fuzzy Affair with DNA

(2021) Mohamed Ghoneim et al.   TRENDS IN BIOCHEMICAL SCIENCES

Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants

(2021) Xiaomin Ni et al.   ACS Chemical Biology

Chemical Inhibition of ENL/AF9 YEATS Domains in Acute Leukemia

(2021) Leopold Garnar-Wortzel et al.   ACS Central Science

Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

(2021) Yunhui Peng et al.   Nature Communications

Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers

(2021) Kendra R. Vann et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Impaired cell fate through gain-of-function mutations in a chromatin reader

(2019) Liling Wan et al.   NATURE

PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles

(2018) Federico Fogolari et al.   Journal of Chemical Information and Modeling

The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

(2018) Emma A Morrison et al.   eLife

Discovery of an MLLT1/3 YEATS Domain Chemical Probe

(2018) Moses Moustakim et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Avoiding False Positive Conclusions in Molecular Simulation: The Importance of Replicas

(2018) Bernhard Knapp et al.   Journal of Chemical Theory and Computation

Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL)

(2018) David Heidenreich et al.   JOURNAL OF MEDICINAL CHEMISTRY

Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains

(2018) Tyler Weaver et al.   MOLECULES

Structural insights into the π-π-π stacking mechanism and DNA-binding activity of the YEATS domain

(2018) Brianna J. Klein et al.   Nature Communications

YEATS Domain—A Histone Acylation Reader in Health and Disease

(2017) Dan Zhao et al.   JOURNAL OF MOLECULAR BIOLOGY

Transcription control by the ENL YEATS domain in acute leukaemia

(2017) Michael A. Erb et al.   NATURE

ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia

(2017) Liling Wan et al.   NATURE

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor

(2017) Samantha Gadd et al.   NATURE GENETICS

Insights into newly discovered marks and readers of epigenetic information

(2016) Forest H Andrews et al.   Nature Chemical Biology

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

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

MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours

(2015) Elizabeth J. Perlman et al.   Nature Communications

AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation

(2014) Yuanyuan Li et al.   CELL

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

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

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail

(2012) George V. Papamokos et al.   BIOPHYSICAL JOURNAL

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Comparing Conformational Ensembles Using the Kullback–Leibler Divergence Expansion

(2012) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

YEATS domain proteins: a diverse family with many links to chromatin modification and transcriptionThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

(2009) Julia M. Schulze et al.   Biochemistry and Cell Biology

Large-scale efficient Langevin dynamics, and why it works

(2009) Jiayu Dai et al.   EPL

Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles

(2009) Christopher L. McClendon et al.   Journal of Chemical Theory and Computation

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS