The energy landscape of adenylate kinase during catalysis

Computational Enzyme Design

(2013) Gert Kiss et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Hydrogen Tunneling Links Protein Dynamics to Enzyme Catalysis

(2013) Judith P. Klinman et al.   Annual Review of Biochemistry

Global Transitions of Proteins Explored by a Multiscale Hybrid Methodology: Application to Adenylate Kinase

(2013) Mert Gur et al.   BIOPHYSICAL JOURNAL

Precision is essential for efficient catalysis in an evolved Kemp eliminase

(2013) Rebecca Blomberg et al.   NATURE

Divergent evolution of protein conformational dynamics in dihydrofolate reductase

(2013) Gira Bhabha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Why nature really chose phosphate

(2013) Shina C. L. Kamerlin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

The Structural Basis for Control of Eukaryotic Protein Kinases

(2012) Jane A. Endicott et al.   Annual Review of Biochemistry

Optimal simultaneous superpositioning of multiple structures with missing data

(2012) Douglas L. Theobald et al.   BIOINFORMATICS

Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates

(2012) Yong Wang et al.   Journal of Chemical Theory and Computation

Iterative approach to computational enzyme design

(2012) H. K. Privett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM

(2011) T. Geoff G. Battye et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis

(2011) Jonathan K. Lassila et al.   Annual Review of Biochemistry

Quantifying Density Fluctuations in Volumes of All Shapes and Sizes Using Indirect Umbrella Sampling

(2011) Amish J. Patel et al.   JOURNAL OF STATISTICAL PHYSICS

Catalytic Control in the EGF Receptor and Its Connection to General Kinase Regulatory Mechanisms

(2011) Natalia Jura et al.   MOLECULAR CELL

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

(2011) A. J. Adamczyk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis

(2011) G. Bhabha et al.   SCIENCE

Briefly Bound to Activate: Transient Binding of a Second Catalytic Magnesium Activates the Structure and Dynamics of CDK2 Kinase for Catalysis

(2011) Zhao Qin Bao et al.   STRUCTURE

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics

(2010) Pavel V. Afonine et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

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

(2010) Nohad Gresh et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protonation States of the Key Active Site Residues and Structural Dynamics of theglmSRiboswitch As Revealed by Molecular Dynamics

(2010) Pavel Banáš et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis

(2010) Matthew J. Cliff et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics connect substrate recognition to catalysis in protein kinase A

(2010) Larry R Masterson et al.   Nature Chemical Biology

Why did Nature select phosphate for its dominant roles in biology?

(2010) Matthew W. Bowler et al.   NEW JOURNAL OF CHEMISTRY

Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by Formula rather than by phosphoranes

(2010) N. J. Baxter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of CASK into a Mg2+-Sensitive Kinase

(2010) K. Mukherjee et al.   Science Signaling

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

(2009) Mark A. Ditzler et al.   ACCOUNTS OF CHEMICAL RESEARCH

Cobalt-, zinc- and iron-bound forms of adenylate kinase (AK) from the sulfate-reducing bacteriumDesulfovibrio gigas: purification, crystallization and preliminary X-ray diffraction analysis

(2009) A. V. Kladova et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

A Transition Path Ensemble Study Reveals a Linchpin Role for Mg2+during Rate-Limiting ADP Release from Protein Kinase A

(2009) Ilja V. Khavrutskii et al.   BIOCHEMISTRY

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

An integrated model for enzyme catalysis emerges from studies of hydrogen tunneling

(2009) Judith P. Klinman   CHEMICAL PHYSICS LETTERS

Tyrosine phosphorylation: thirty years and counting

(2009) Tony Hunter   CURRENT OPINION IN CELL BIOLOGY

The Intrinsic Reactivity of ATP and the Catalytic Proficiencies of Kinases Acting on Glucose,N-Acetylgalactosamine, and Homoserine

(2009) Randy B. Stockbridge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Linear Energy Relationships for the Octahedral Preference of Mg, Ca and Transition Metal Ions

(2009) George Pontikis et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM

(2009) Pavel Banáš et al.   METHODS

Enzymatic transition states and dynamic motion in barrier crossing

(2009) Steven D Schwartz et al.   Nature Chemical Biology

A 21st century revisionist's view at a turning point in enzymology

(2009) Zachary D Nagel et al.   Nature Chemical Biology

Whether proton transition to the triphosphate tail of ATP occurs at protein kinase environment: A Car-Parrinello ab initio molecular dynamics study

(2008) Sheng-Yong Yang et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Direct Mg2+Binding Activates Adenylate Kinase fromEscherichia coli

(2008) Yan-Wen Tan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Anionic Charge Is Prioritized over Geometry in Aluminum and Magnesium Fluoride Transition State Analogs of Phosphoryl Transfer Enzymes

(2008) Nicola J. Baxter et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

Computational Study of the Force Dependence of Phosphoryl Transfer during DNA Synthesis by a High Fidelity Polymerase

(2008) Ravindra Venkatramani et al.   PHYSICAL REVIEW LETTERS