(Q26781547)

1

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Sophia P Hirakis

2

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Lane W Votapka

3

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Robert D Malmstrom

4

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Rommie E Amaro

5

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Andrew D McCulloch

6

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language of work or name

English

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publication date

2015

0 references

published in

Frontiers in Physiology

1 reference

Molecular insights into arrhythmogenic right ventricular cardiomyopathy caused by plakophilin-2 missense mutations

volume

6

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page(s)

250

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

CHARMM: the biomolecular simulation program

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Electrostatics of nanosystems: application to microtubules and the ribosome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Markov state models of biomolecular conformational dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

The ensemble nature of allostery

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Modeling protein association mechanisms and kinetics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

PKA-I holoenzyme structure reveals a mechanism for cAMP-dependent activation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Scalable molecular dynamics with NAMD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

A compartmentalized mathematical model of the β1-adrenergic signaling system in mouse ventricular myocytes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Atomic-level characterization of the structural dynamics of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

The role of dynamic conformational ensembles in biomolecular recognition

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Dynamic personalities of proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Classical electrostatics in biology and chemistry

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Enhanced sampling techniques in molecular dynamics simulations of biological systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Using Markov state models to develop a mechanistic understanding of protein kinase A regulatory subunit RIα activation in response to cAMP binding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Lipid14: The Amber Lipid Force Field.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Markov modeling of ion channels: implications for understanding disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Computational modeling of subcellular transport and signaling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Probing the diverse landscape of protein flexibility and binding

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Spatial modeling of cell signaling networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Browndye: A Software Package for Brownian Dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Protein stability, flexibility and function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Coupling of adjacent tropomyosins enhances cross-bridge-mediated cooperative activation in a markov model of the cardiac thin filament

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

A-kinase anchoring proteins: getting to the heart of the matter.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Atomically detailed simulation of the recovery stroke in myosin by Milestoning

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

A transition path ensemble study reveals a linchpin role for Mg(2+) during rate-limiting ADP release from protein kinase A.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Virtual Cell modelling and simulation software environment.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Comparison of protein force fields for molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

A milestoning study of the kinetics of an allosteric transition: atomically detailed simulations of deoxy Scapharca hemoglobin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Pharmacogenetics and anti-arrhythmic drug therapy: a theoretical investigation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Computational biology in the study of cardiac ion channels and cell electrophysiology.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Molecular dynamics: survey of methods for simulating the activity of proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

The GROMOS software for biomolecular simulation: GROMOS05.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Force fields for protein simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

cAMP analog mapping of Epac1 and cAMP kinase. Discriminating analogs demonstrate that Epac and cAMP kinase act synergistically to promote PC-12 cell neurite extension

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Molecular dynamics simulations of biomolecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Biomolecular diffusional association

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Na(+) channel mutation that causes both Brugada and long-QT syndrome phenotypes: a simulation study of mechanism

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Folding funnels, binding funnels, and protein function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Brownian dynamics simulation of protein-protein diffusional encounter

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Estimating single-channel kinetic parameters from idealized patch-clamp data containing missed events

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Brownian dynamics simulations of molecular recognition in an antibody-antigen system

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Revisiting and computing reaction coordinates with Directional Milestoning

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Milestoning without a Reaction Coordinate

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Simulation of the diffusional association of barnase and barstar.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4563169

Structural basis for the mutation-induced dysfunction of human CYP2J2: a computational study.

19 June 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

β blockers in hypertension

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Brownian dynamics simulations on CPU and GPU with BD_BOX.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Graphs, random sums, and sojourn time distributions, with application to ion-channel modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Computing time scales from reaction coordinates by milestoning.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Synthesis of generalized algorithms for the fast computation of synaptic conductances with Markov kinetic models in large network simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Active site mutations define the pathway for the cooperative activation of cAMP-dependent protein kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Role of magnesium-ATP in the activation and reassociation of cAMP-dependent protein kinase I: consequences of replacing the essential arginine in cAMP-binding site A

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Markov models of molecular kinetics: generation and validation

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Modeling beta-adrenergic control of cardiac myocyte contractility in silico

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Transition state theory: variational formulation, dynamical corrections, and error estimates.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

On the assumptions underlying milestoning

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Dynamic properties of force fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Erratum: The role of dynamic conformational ensembles in biomolecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Linking a genetic defect to its cellular phenotype in a cardiac arrhythmia

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250

Molecular simulations of diffusion and association in multimacromolecular systems

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26441670

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26441670

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A computational framework for derivative-free optimization of cardiovascular geometries

1 reference

https://api.crossref.org/works/10.3389%2FFPHYS.2015.00250