Constant pressure molecular dynamics for molecular systems
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December 1983 |
Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 Å resolution
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March 1992 |
Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis
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phenix.model_vs_data : a high-level tool for the calculation of crystallographic model and data statistics
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Electrostatics of nanosystems: Application to microtubules and the ribosome
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August 2001 |
Kemp elimination catalysts by computational enzyme design
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March 2008 |
Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase
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October 2013 |
Overview of the CCP 4 suite and current developments
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March 2011 |
Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis
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May 2010 |
Quantifying Density Fluctuations in Volumes of All Shapes and Sizes Using Indirect Umbrella Sampling
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August 2011 |
Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis
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June 2013 |
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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February 2008 |
Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase
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November 2005 |
Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
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July 2011 |
Fpocket: An open source platform for ligand pocket detection
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January 2009 |
An NMR Perspective on Enzyme Dynamics
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August 2006 |
Why nature chose phosphates
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March 1987 |
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
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November 2007 |
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
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April 1998 |
Constant pressure molecular dynamics simulation: The Langevin piston method
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September 1995 |
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
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August 2011 |
Intrinsic motions along an enzymatic reaction trajectory
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November 2007 |
Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by Formula rather than by phosphoranes
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February 2010 |
The time scale of the catalytic loop motion in triosephosphate isomerase11Edited by P. E. Wright
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June 2001 |
Enzymatic transition states and dynamic motion in barrier crossing
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July 2009 |
A Perspective on Enzyme Catalysis
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August 2003 |
A modified TIP3P water potential for simulation with Ewald summation
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November 2004 |
A 21st century revisionist's view at a turning point in enzymology
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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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June 1993 |
NMR View: A computer program for the visualization and analysis of NMR data
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September 1994 |
Coot model-building tools for molecular graphics
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November 2004 |
Iterative approach to computational enzyme design
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February 2012 |
Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect
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August 1971 |
Dynamics connect substrate recognition to catalysis in protein kinase A
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October 2010 |
Cyclic AMP-dependent ATPase activity of bovine heart protein kinase.
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February 1979 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution
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January 2010 |
Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
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September 1998 |
Polymorphic transitions in single crystals: A new molecular dynamics method
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December 1981 |
The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA
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March 2006 |
The Intrinsic Reactivity of ATP and the Catalytic Proficiencies of Kinases Acting on Glucose, N -Acetylgalactosamine, and Homoserine : A THERMODYNAMIC ANALYSIS
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June 2009 |
Precision is essential for efficient catalysis in an evolved Kemp eliminase
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October 2013 |
Whether proton transition to the triphosphate tail of ATP occurs at protein kinase environment: A Car-Parrinello ab initio molecular dynamics study
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January 2008 |
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
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November 1995 |
Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli
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June 1987 |
An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling
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March 2009 |
Direct Measurements of the Dissociation-Rate Constant for Inhibitor-Enzyme Complexes via the T1ρ and T2 (CPMG) Methods
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July 1994 |
The CCPN data model for NMR spectroscopy: Development of a software pipeline
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April 2005 |
Evolution of CASK into a Mg2+-Sensitive Kinase
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April 2010 |
VMD: Visual molecular dynamics
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February 1996 |
Computational Enzyme Design
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March 2013 |
Electrostatic Basis for Enzyme Catalysis
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August 2006 |
Scalable molecular dynamics with NAMD
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January 2005 |
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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March 1977 |
A Transition Path Ensemble Study Reveals a Linchpin Role for Mg 2+ during Rate-Limiting ADP Release from Protein Kinase A
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December 2009 |
Enzymatic Mechanisms of Phosphate and Sulfate Transfer
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August 2006 |
Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study
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April 2010 |
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
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February 1996 |
NMR Characterization of the Dynamics of Biomacromolecules
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August 2004 |
The closed conformation of a highly flexible protein: The structure ofE. coli adenylate kinase with bound AMP and AMPPNP
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July 1994 |
Optimal simultaneous superpositioning of multiple structures with missing data
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April 2012 |
Tyrosine phosphorylation: thirty years and counting
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April 2009 |
Why nature really chose phosphate
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January 2013 |
Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis
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September 1994 |
Scaling and assessment of data quality
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December 2005 |
A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis
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April 2011 |
Development and current status of the CHARMM force field for nucleic acids
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January 2000 |
The Structural Basis for Control of Eukaryotic Protein Kinases
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July 2012 |
Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates
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November 2012 |
GTPase mechanism of Gproteins from the 1.7-Å crystal structure of transducin α - GDP AIF−4
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November 1994 |
Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair
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August 2004 |
Why did Nature select phosphate for its dominant roles in biology?
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January 2010 |
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
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March 2011 |
A molecular dynamics method for simulations in the canonical ensemble
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June 1984 |
LINCS: A linear constraint solver for molecular simulations
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September 1997 |
Enzyme-Catalyzed Phosphoryl Transfer Reactions
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June 1980 |
Features and development of Coot
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March 2010 |
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
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July 1983 |
Kinetic and Catalytic Mechanisms of Protein Kinases
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August 2001 |
REFMAC 5 for the refinement of macromolecular crystal structures
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March 2011 |
Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms
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April 2011 |
Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM
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October 2009 |
Canonical dynamics: Equilibrium phase-space distributions
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March 1985 |
The Static Magnetic Field Dependence of Chemical Exchange Linebroadening Defines the NMR Chemical Shift Time Scale
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March 2000 |
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
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October 1992 |
Divergent evolution of protein conformational dynamics in dihydrofolate reductase
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September 2013 |
Metal Activation of Enzymes in Nucleic Acid Biochemistry
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May 1998 |
Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In
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January 2010 |
Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)
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August 2010 |
Anionic Charge Is Prioritized over Geometry in Aluminum and Magnesium Fluoride Transition State Analogs of Phosphoryl Transfer Enzymes
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March 2008 |
Constant pressure molecular dynamics algorithms
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September 1994 |
Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics
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July 2010 |
Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacterium Desulfovibrio gigas : purification, crystallization and preliminary X-ray diffraction analysis
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August 2009 |
Phaser crystallographic software
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July 2007 |
Linear Energy Relationships for the Octahedral Preference of Mg, Ca and Transition Metal Ions
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April 2009 |
At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?
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January 2010 |
NMR Characterization of the Dynamics of Biomacromolecules
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November 2004 |
Enzymatic Mechanisms of Phosphate and Sulfate Transfer
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October 2006 |
Computational studies of polyurethanases from Pseudomonas
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January 2021 |
PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
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December 2019 |
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
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February 2021 |
Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity
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March 2021 |
Spontaneous drying of non-polar deep-cavity cavitand pockets in aqueous solution
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May 2020 |
Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases
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January 2021 |
Overview of the CCP4 suite and current developments.
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text
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January 2011 |
A molecular dynamics method for simulations in the canonical ensemble
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journal
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January 2002 |
Why did nature select phosphate for its dominant roles in biology?
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journal
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July 2010 |
Precision is essential for efficient catalysis in an evolved Kemp eliminase
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text
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January 2013 |
Electrostatic Basis for Enzyme Catalysis
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journal
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October 2006 |
The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA
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text
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January 2006 |
A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides
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January 1997 |
An NMR Perspective on Enzyme Dynamics
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October 2006 |
Chemical exchange and nmr T2 relaxation—The multisite case
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April 1978 |
Fast Sampling of A-to-B Protein Global Conformational Transitions: From Galileo Galilei to Monte Carlo Anisotropic Network Modeling
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October 2013 |
Mechanism and Catalysis of Nucleophilic Substitution in Phosphate Esters
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book
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January 1989 |
Signaling mechanistics: Aluminum fluoride for molecule of the year
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November 1997 |
“Eppur si muove” (yet it moves)
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September 2011 |
Mechanism of Activation of ERK2 by Dual Phosphorylation
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October 2000 |
Direct Mg 2+ Binding Activates Adenylate Kinase from Escherichia coli
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November 2008 |
Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase
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February 2008 |
PHENIX: a comprehensive Python-based system for macromolecular structure solution.
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text
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January 2010 |