Variational cross-validation of slow dynamical modes in molecular kinetics

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Markov state models of biomolecular conformational dynamics

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

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

Statistical Model Selection for Markov Models of Biomolecular Dynamics

(2014) Robert T. McGibbon et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

(2014) Om P Choudhary et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on Ab Initio Target Data

(2013) Lei Huang et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

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

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

Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling

(2013) A. H. Phillips et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

(2012) Gregory R. Bowman   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

(2012) Ting Zhou et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data

(2012) Lee-Ping Wang et al.   Journal of Chemical Theory and Computation

An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations

(2012) Ernesto Vargas et al.   JOURNAL OF GENERAL PHYSIOLOGY

Evaluation and Optimization of Discrete State Models of Protein Folding

(2012) Elizabeth H. Kellogg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Kinetic characterization of the critical step in HIV-1 protease maturation

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

Simple few-state models reveal hidden complexity in protein folding

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

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sparse Discriminant Analysis

(2011) Line Clemmensen et al.   TECHNOMETRICS

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

(2010) I. Buch et al.   Journal of Chemical Information and Modeling

A Bayesian method for construction of Markov models to describe dynamics on various time-scales

(2010) Emily K. Rains et al.   JOURNAL OF CHEMICAL PHYSICS

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A majorization-minimization approach to the sparse generalized eigenvalue problem

(2010) Bharath K. Sriperumbudur et al.   MACHINE LEARNING

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

(2010) Vijay S. Pande et al.   METHODS

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Identification of the protein folding transition state from molecular dynamics trajectories

(2009) S. Muff et al.   JOURNAL OF CHEMICAL PHYSICS

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

(2009) Sergio Bacallado et al.   JOURNAL OF CHEMICAL PHYSICS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Using Markov Models to Simulate Electron Spin Resonance Spectra from Molecular Dynamics Trajectories

(2008) Deniz Sezer et al.   JOURNAL OF PHYSICAL CHEMISTRY B