In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity inSEDPHAT

(2015) Huaying Zhao et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

QM/MM Modelling of Drug-Metabolizing Enzymes

(2014) Richard Lonsdale et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Double trouble-Buffer selection and His-tag presence may be responsible for nonreproducibility of biomedical experiments

(2014) Karolina A. Majorek et al.   PROTEIN SCIENCE

Understanding the apparent stator-rotor connections in the rotary ATPase family using coarse-grained computer modeling

(2014) Robin A. Richardson et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

(2014) Richard Lonsdale et al.   PLoS Computational Biology

Analysis and Assay of Oseltamivir-Resistant Mutants of Influenza Neuraminidase via Direct Observation of Drug Unbinding and Rebinding in Simulation

(2013) Christopher J. Woods et al.   BIOCHEMISTRY

Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Methods in Computational Enzymology

(2013) Marc W. van der Kamp et al.   BIOCHEMISTRY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Cryo-electron tomography: The challenge of doing structural biology in situ

(2013) Vladan Lučić et al.   JOURNAL OF CELL BIOLOGY

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions

(2013) M. Gur et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

A stochastic finite element model for the dynamics of globular macromolecules

(2013) Robin C. Oliver et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Quantum Mechanics/Molecular Mechanics Modeling of Regioselectivity of Drug Metabolism in Cytochrome P450 2C9

(2013) Richard Lonsdale et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

(2013) Gongpu Zhao et al.   NATURE

Self-Assembling Cages from Coiled-Coil Peptide Modules

(2013) J. M. Fletcher et al.   SCIENCE

Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors

(2013) Thomas L. Rodgers et al.   PLOS BIOLOGY

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

A practical guide to modelling enzyme-catalysed reactions

(2012) Richard Lonsdale et al.   CHEMICAL SOCIETY REVIEWS

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

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

Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions

(2012) Richard Lonsdale et al.   Journal of Chemical Theory and Computation

Protein activity regulation by conformational entropy

(2012) Shiou-Ru Tzeng et al.   NATURE

Equilibrium Sampling in Biomolecular Simulations

(2011) Daniel M. Zuckerman   Annual Review of Biophysics

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers

(2011) P. Marius et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

(2011) Mario Orsi et al.   PLoS One

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Protein folding on the ribosome

(2010) Lisa D Cabrita et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

(2010) Kara E. Ranaghan et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

Inclusion of Dispersion Effects Significantly Improves Accuracy of Calculated Reaction Barriers for Cytochrome P450 Catalyzed Reactions

(2010) Richard Lonsdale et al.   Journal of Physical Chemistry Letters

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies

(2010) Do-Nyun Kim et al.   NUCLEIC ACIDS RESEARCH

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories

(2010) Tim Meyer et al.   STRUCTURE

Calorimetry and Thermodynamics in Drug Design

(2008) Jonathan B. Chaires   Annual Review of Biophysics

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

(2008) Kathryn A. Scott et al.   STRUCTURE