Bridging scales through multiscale modeling: a case study on protein kinase A

DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

(2016) Lane W. Votapka et al.   Communications in Computational Physics

Enhanced sampling techniques in molecular dynamics simulations of biological systems

(2015) Rafael C. Bernardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

38 Multiscale estimation of binding kinetics using molecular dynamics, brownian dynamics, and milestoning

(2015) Lane W. Votapka et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

(2015) Mauro L. Mugnai et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

Allostery through the computational microscope: cAMP activation of a canonical signalling domain

(2015) Robert D. Malmstrom et al.   Nature Communications

Computational modeling of subcellular transport and signaling

(2014) Johan Hake et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Using Markov State Models to Develop a Mechanistic Understanding of Protein Kinase A Regulatory Subunit RIα Activation in Response to cAMP Binding

(2014) Britton W. Boras et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipid14: The Amber Lipid Force Field

(2014) Callum J. Dickson et al.   Journal of Chemical Theory and Computation

Application of Molecular-Dynamics Based Markov State Models to Functional Proteins

(2014) Robert D. Malmstrom et al.   Journal of Chemical Theory and Computation

Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide

(2014) Panagiotis I. Koukos et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

A Compartmentalized Mathematical Model of the β1-Adrenergic Signaling System in Mouse Ventricular Myocytes

(2014) Vladimir E. Bondarenko   PLoS One

Modeling protein association mechanisms and kinetics

(2013) Huan-Xiang Zhou et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study

(2013) Shan Cong et al.   Journal of Chemical Information and Modeling

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

(2013) Johannes Schöneberg et al.   PLoS One

Molecular Insights into Arrhythmogenic Right Ventricular Cardiomyopathy Caused by Plakophilin-2 Missense Mutations

(2012) Florian Kirchner et al.   Circulation-Cardiovascular Genetics

Probing the diverse landscape of protein flexibility and binding

(2012) Joseph A Marsh et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce 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

Phospholemman is a negative feed-forward regulator of Ca2+ in β-adrenergic signaling, accelerating β-adrenergic inotropy

(2012) Jason H. Yang et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Unassisted Transport of N-Acetyl-l-tryptophanamide through Membrane: Experiment and Simulation of Kinetics

(2012) Alfredo E. Cardenas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Discussion of Multicyclic Hubbert Modeling as a Method for Forecasting Future Petroleum Production

(2011) Ken B. Anderson et al.   ENERGY & FUELS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Brownian dynamics simulations on CPU and GPU with BD_BOX

(2011) Maciej Długosz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Kinetic modeling of Nav1.7 provides insight into erythromelalgia-associated F1449V mutation

(2011) Meron Gurkiewicz et al.   JOURNAL OF NEUROPHYSIOLOGY

Revisiting and Computing Reaction Coordinates with Directional Milestoning

(2011) Serdal Kirmizialtin et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Interaction of fast and slow dynamics in endocrine control systems with an application to β-cell dynamics

(2011) Yi-Fang Wang et al.   MATHEMATICAL BIOSCIENCES

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package

(2011) Tihamér Geyer   BMC Biophysics

Protein stability, flexibility and function

(2010) Kaare Teilum et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Coupling of Adjacent Tropomyosins Enhances Cross-Bridge-Mediated Cooperative Activation in a Markov Model of the Cardiac Thin Filament

(2010) Stuart G. Campbell et al.   BIOPHYSICAL JOURNAL

A-Kinase Anchoring Proteins

(2010) John D. Scott et al.   CIRCULATION

Browndye: A software package for Brownian dynamics

(2010) Gary A. Huber et al.   COMPUTER PHYSICS COMMUNICATIONS

Mutations and polymorphisms in the gene encoding regulatory subunit type 1-alpha of protein kinase A (PRKAR1A): an update

(2010) Anélia Horvath et al.   HUMAN MUTATION

Milestoning without a Reaction Coordinate

(2010) Peter Májek et al.   Journal of Chemical Theory and Computation

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

β blockers in hypertension

(2010) John M Cruickshank   LANCET

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

(2010) R. Elber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities

(2010) David Cregut et al.   PROTEIN SCIENCE

Dissecting the cAMP-inducible allosteric switch in protein kinase A RIα

(2010) Timothy J. Sjoberg et al.   PROTEIN SCIENCE

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

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

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Erratum: The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

A computational framework for derivative-free optimization of cardiovascular geometries

(2008) Alison L. Marsden et al.   COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING

Virtual Cell modelling and simulation software environment

(2008) I.I. Moraru et al.   IET Systems Biology

On the assumptions underlying milestoning

(2008) Eric Vanden-Eijnden et al.   JOURNAL OF CHEMICAL PHYSICS

Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces

(2008) Rex A. Kerr et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING