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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Nature communications, 2022-10, Vol.13 (1), p.5884-24, Article 5884

2022

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Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position

Proteins, structure, function, and bioinformatics, 2016-10, Vol.84 (10), p.1480-1489

2016

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Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2023-06, Vol.127 (25), p.5470-5490

2023

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Modeling conformational ensembles of slow functional motions in Pin1-WW

PLoS computational biology, 2010-12, Vol.6 (12), p.e1001015-e1001015

2010

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A comparison of weighted ensemble and Markov state model methodologies

The Journal of chemical physics, 2015-06, Vol.142 (21), p.214113-214113

2015

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Evaluation of conformational changes in diabetes-associated mutation in insulin a chain: A molecular dynamics study

Proteins, structure, function, and bioinformatics, 2015-04, Vol.83 (4), p.662-669

2015

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Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods

Journal of chemical information and modeling, 2023-09, Vol.63 (17), p.5408-5432

2023

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Normal mode partitioning of Langevin dynamics for biomolecules

The Journal of chemical physics, 2008-04, Vol.128 (14), p.145101-145101-13

2008

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AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble

Journal of chemical information and modeling, 2014-10, Vol.54 (10), p.3033-3043

2014

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Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

IEEE/ACM transactions on computational biology and bioinformatics, 2007-01, Vol.4 (1), p.78-87

2007

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A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis

Journal of chemical information and modeling, 2023-07, Vol.63 (13), p.4115-4124

2023

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Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach

Malaria journal, 2014-11, Vol.13 (1), p.434-434, Article 434

2014

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From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development

Computing in science & engineering, 2007-07, Vol.9 (4), p.50-60

2007

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A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis

Computer physics communications, 2007-06, Vol.176 (11), p.670-681

2007

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Long Timestep Molecular Dynamics on the Graphical Processing Unit

Journal of chemical theory and computation, 2013-08, Vol.9 (8), p.3267-3281

2013

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A separable shadow Hamiltonian hybrid Monte Carlo method

The Journal of chemical physics, 2009-11, Vol.131 (17), p.174106-174106-7

2009

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Accelerating the replica exchange method through an efficient all-pairs exchange

The Journal of chemical physics, 2007-02, Vol.126 (7), p.074103-074103

2007

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Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules

Journal of computational physics, 2004-11, Vol.200 (2), p.581-604

2004

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MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms

Journal of computational chemistry, 2005-07, Vol.26 (10), p.1021-1031

2005

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Belief Propagation Estimation of Protein and Domain Interactions Using the Sum-Product Algorithm

IEEE transactions on information theory, 2010-02, Vol.56 (2), p.742-755

2010

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Identification of novel arthropod vector G protein-coupled receptors

Parasites & vectors, 2013-05, Vol.6 (1), p.150-150, Article 150

2013

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MDL, A Domain-Specific Language for Molecular Dynamics

40th Annual Simulation Symposium (ANSS'07), 2007, p.256-266

2007

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MDLab: A molecular dynamics simulation prototyping environment

Journal of computational chemistry, 2010-05, Vol.31 (7), p.1345-1356

2010

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Verlet-I/R-RESPA/Impulse is limited by nonlinear instabilities

SIAM journal on scientific computing, 2003, Vol.24 (6), p.1951-1973

2003

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A framework for three-dimensional simulation of morphogenesis

IEEE/ACM transactions on computational biology and bioinformatics, 2005-10, Vol.2 (4), p.273-288

2005

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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position

Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories

Modeling conformational ensembles of slow functional motions in Pin1-WW

A comparison of weighted ensemble and Markov state model methodologies

Evaluation of conformational changes in diabetes-associated mutation in insulin a chain: A molecular dynamics study

Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods

Normal mode partitioning of Langevin dynamics for biomolecules

AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble

Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis

Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach

From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development

A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis

Long Timestep Molecular Dynamics on the Graphical Processing Unit

A separable shadow Hamiltonian hybrid Monte Carlo method

Accelerating the replica exchange method through an efficient all-pairs exchange

Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules

MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms

Belief Propagation Estimation of Protein and Domain Interactions Using the Sum-Product Algorithm

Identification of novel arthropod vector G protein-coupled receptors

MDL, A Domain-Specific Language for Molecular Dynamics

MDLab: A molecular dynamics simulation prototyping environment

Verlet-I/R-RESPA/Impulse is limited by nonlinear instabilities

A framework for three-dimensional simulation of morphogenesis

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