Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme
|
journal
|
January 2017 |
Protein folded states are kinetic hubs
|
journal
|
June 2010 |
Long-timescale molecular dynamics simulations of protein structure and function
|
journal
|
April 2009 |
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
|
journal
|
May 1997 |
Global Kinetic Explorer: A new computer program for dynamic simulation and fitting of kinetic data
|
journal
|
April 2009 |
Integrative, dynamic structural biology at atomic resolution—it's about time
|
journal
|
March 2015 |
Structural basis for activity regulation of MLL family methyltransferases
|
journal
|
February 2016 |
Kinetic Distance and Kinetic Maps from Molecular Dynamics Simulation
|
journal
|
September 2015 |
Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8
|
journal
|
December 2016 |
Unravelling biological macromolecules with cryo-electron microscopy
|
journal
|
September 2016 |
Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models
|
journal
|
November 2017 |
Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling
|
journal
|
October 2016 |
Structural origins for the product specificity of SET domain protein methyltransferases
|
journal
|
December 2008 |
Automatic atom type and bond type perception in molecular mechanical calculations
|
journal
|
October 2006 |
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank
|
journal
|
September 2004 |
Towards automated crystallographic structure refinement with phenix.refine
|
journal
|
March 2012 |
Comparison of simple potential functions for simulating liquid water
|
journal
|
July 1983 |
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
|
journal
|
November 2012 |
Kinase inhibitors: the road ahead
|
journal
|
March 2018 |
Variational Approach to Molecular Kinetics
|
journal
|
March 2014 |
A Glimpse of Structural Biology through X-Ray Crystallography
|
journal
|
November 2014 |
Variational cross-validation of slow dynamical modes in molecular kinetics
|
journal
|
March 2015 |
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
|
journal
|
April 2016 |
Energetic dissection of Gleevec's selectivity toward human tyrosine kinases
|
journal
|
September 2014 |
Purification and Functional Characterization of SET8, a Nucleosomal Histone H4-Lysine 20-Specific Methyltransferase
|
journal
|
July 2002 |
XDS
|
journal
|
January 2010 |
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information
|
journal
|
October 2017 |
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
|
journal
|
October 2015 |
Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
|
journal
|
January 2014 |
Activation pathway of Src kinase reveals intermediate states as targets for drug design
|
journal
|
March 2014 |
Quantitative comparison of adaptive sampling methods for protein dynamics
|
journal
|
December 2018 |
Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)
|
journal
|
May 2015 |
Ras Conformational Ensembles, Allostery, and Signaling
|
journal
|
January 2016 |
Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies
|
journal
|
July 2013 |
Markov models of molecular kinetics: Generation and validation
|
journal
|
May 2011 |
PRODRG : a tool for high-throughput crystallography of protein–ligand complexes
|
journal
|
July 2004 |
Comparative Protein Modelling by Satisfaction of Spatial Restraints
|
journal
|
December 1993 |
A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems
|
journal
|
January 2013 |
Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes
|
journal
|
July 2011 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
|
journal
|
June 1993 |
Modulation of p53 Function by SET8-Mediated Methylation at Lysine 382
|
journal
|
August 2007 |
MolProbity : all-atom structure validation for macromolecular crystallography
|
journal
|
December 2009 |
Coot model-building tools for molecular graphics
|
journal
|
November 2004 |
Dynamic Methylation of Numb by Set8 Regulates Its Binding to p53 and Apoptosis
|
journal
|
May 2013 |
Specificity and mechanism of the histone methyltransferase Pr-Set7
|
journal
|
June 2005 |
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling
|
journal
|
June 2017 |
Optimized parameter selection reveals trends in Markov state models for protein folding
|
journal
|
November 2016 |
The expanding landscape of ‘oncohistone’ mutations in human cancers
|
journal
|
March 2019 |
The emerging role of lysine methyltransferase SETD8 in human diseases
|
journal
|
September 2016 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution
|
journal
|
January 2010 |
Epigenetic siRNA and Chemical Screens Identify SETD8 Inhibition as a Therapeutic Strategy for p53 Activation in High-Risk Neuroblastoma
|
journal
|
January 2017 |
Ion-water interaction potentials derived from free energy perturbation simulations
|
journal
|
October 1990 |
IPython: A System for Interactive Scientific Computing
|
journal
|
January 2007 |
Association of functional polymorphism at the miR-502-binding site in the 3′ untranslated region of the SETD8 gene with risk of childhood acute lymphoblastic leukemia, a preliminary report
|
journal
|
July 2014 |
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
|
journal
|
June 2008 |
Discovery of a Selective, Substrate-Competitive Inhibitor of the Lysine Methyltransferase SETD8
|
journal
|
July 2014 |
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
|
journal
|
February 2015 |
Matplotlib: A 2D Graphics Environment
|
journal
|
January 2007 |
Modelling proteins’ hidden conformations to predict antibiotic resistance
|
journal
|
October 2016 |
Python for Scientific Computing
|
journal
|
January 2007 |
Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain
|
journal
|
November 2017 |
The cancer epigenome: Concepts, challenges, and therapeutic opportunities
|
journal
|
March 2017 |
Python for Scientists and Engineers
|
journal
|
March 2011 |
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
|
journal
|
July 2017 |
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
|
journal
|
June 2016 |
PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription
|
journal
|
February 2012 |
Molecular Mechanisms of Disease-Causing Missense Mutations
|
journal
|
November 2013 |
Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes
|
journal
|
September 2018 |
GPCR Dynamics: Structures in Motion
|
journal
|
June 2016 |
Probing Protein Folding and Conformational Transitions with Fluorescence
|
journal
|
May 2006 |
Computer simulations of NaCl association in polarizable water
|
journal
|
March 1994 |
A High Throughput Scintillation Proximity Imaging Assay for Protein Methyltransferases
|
journal
|
April 2012 |
New Insights in Protein Kinase Conformational Dynamics
|
journal
|
September 2012 |
Improved side-chain torsion potentials for the Amber ff99SB protein force field
|
journal
|
January 2010 |
Structures of Large Protein Complexes Determined by Nuclear Magnetic Resonance Spectroscopy
|
journal
|
May 2017 |
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
|
journal
|
July 2010 |
Small-Molecule Inhibitors of SETD8 with Cellular Activity
|
journal
|
September 2014 |
Combining experimental and simulation data of molecular processes via augmented Markov models
|
journal
|
July 2017 |
MSMBuilder: Statistical Models for Biomolecular Dynamics
|
journal
|
January 2017 |
Retrieval of Crystallographically-Derived Molecular Geometry Information
|
journal
|
November 2004 |
Exploring protein native states and large-scale conformational changes with a modified generalized born model
|
journal
|
March 2004 |
Ordering a Dynamic Protein Via a Small-Molecule Stabilizer
|
journal
|
February 2013 |
Markov State Models: From an Art to a Science
|
journal
|
February 2018 |
Nonmetric multidimensional scaling: A numerical method
|
journal
|
June 1964 |
Development and testing of a general amber force field
|
journal
|
January 2004 |
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
|
journal
|
October 2002 |
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
|
journal
|
October 2015 |
The molecular hallmarks of epigenetic control
|
journal
|
June 2016 |
The winding path of protein methylation research: milestones and new frontiers
|
journal
|
May 2017 |
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
|
journal
|
March 2013 |
Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities
|
journal
|
April 2019 |
Stereochemical errors and their implications for molecular dynamics simulations
|
journal
|
January 2011 |
Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments
|
journal
|
March 2011 |
Features and development of Coot
|
journal
|
March 2010 |
REFMAC 5 for the refinement of macromolecular crystal structures
|
journal
|
March 2011 |
Monte Carlo studies of the dielectric properties of water-like models
|
journal
|
September 1973 |
Caliber Corrected Markov Modeling (C 2 M 2 ): Correcting Equilibrium Markov Models
|
journal
|
January 2018 |
Progress in the Development of Lysine Methyltransferase SETD8 Inhibitors
|
journal
|
July 2016 |
XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density
|
journal
|
April 1999 |
Epigenetic plasticity and the hallmarks of cancer
|
journal
|
July 2017 |
The role of protein dynamics in the evolution of new enzyme function
|
journal
|
September 2016 |
SET8 promotes epithelial-mesenchymal transition and confers TWIST dual transcriptional activities: SET8 promotes TWIST-induced EMT
|
journal
|
October 2011 |
Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2
|
journal
|
April 2016 |
COMPUTING: Screen Savers of the World Unite!
|
journal
|
December 2000 |
Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase
|
journal
|
October 2016 |
Chemical and Biochemical Perspectives of Protein Lysine Methylation
|
journal
|
June 2018 |
Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase
|
journal
|
June 2005 |
Phaser crystallographic software
|
journal
|
July 2007 |
Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell
|
journal
|
January 2016 |
Identification of slow molecular order parameters for Markov model construction
|
journal
|
July 2013 |
Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen
|
journal
|
August 2020 |
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
|
journal
|
December 2019 |
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
|
journal
|
February 2021 |
A genomic and epigenomic atlas of prostate cancer in Asian populations
|
journal
|
March 2020 |
NADPH levels affect cellular epigenetic state by inhibiting HDAC3–Ncor complex
|
journal
|
January 2021 |
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
|
journal
|
April 2016 |
Probing Protein Folding and Conformational Transitions with Fluorescence
|
journal
|
August 2006 |
Specificity and Mechanism of the Histone Methyltransferase Pr-Set7
|
dataset
|
January 2005 |
Purification and Functional Characterization of SET8, a Nucleosomal Histone H4-Lysine 20-Specific Methyltransferase
|
text
|
January 2002 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
|
text
|
January 2010 |
A variational approach to modeling slow processes in stochastic dynamical systems
|
preprint
|
January 2012 |
Variational cross-validation of slow dynamical modes in molecular kinetics
|
text
|
January 2014 |
PR-Set7 Is a Nucleosome-Specific Methyltransferase that Modifies Lysine 20 of Histone H4 and Is Associated with Silent Chromatin
|
journal
|
June 2002 |
Genetic and epigenetic regulation of the NRF2-KEAP1 pathway in human lung cancer
|
journal
|
November 2021 |
Evolutionary Aspects of Enzyme Dynamics
|
journal
|
September 2014 |
MOLREP an Automated Program for Molecular Replacement
|
journal
|
December 1997 |
Solving structures of protein complexes by molecular replacement with Phaser
|
journal
|
December 2006 |
The CCP4 suite programs for protein crystallography
|
journal
|
September 1994 |
wARP : Improvement and Extension of Crystallographic Phases by Weighted Averaging of Multiple-Refined Dummy Atomic Models
|
journal
|
July 1997 |
Beamline 08ID-1, the prime beamline of the Canadian Macromolecular Crystallography Facility
|
journal
|
June 2011 |
Identification of slow molecular order parameters for Markov model construction
|
text
|
January 2013 |
Kinetic distance and kinetic maps from molecular dynamics simulation
|
preprint
|
January 2015 |
DNest4: Diffusive Nested Sampling in C++ and Python
|
preprint
|
January 2016 |
Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
|
preprint
|
January 2018 |
BciPy: Brain-Computer Interface Software in Python
|
preprint
|
January 2020 |
Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning
|
journal
|
May 2018 |