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Takeaways

molecular simulation tools · experimental data analysis · datasets

Molecular simulation tools

Nonequilibrium candidate Monte Carlo (NCMC) example simulation code (Python+OpenMM)

OpenMM Python example simulation code illustrating the use of the nonequilibrium candidate Monte Carlo (NCMC) method for sampling from equilibrium distributions.

This code accompanies the paper:

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David D. L. Minh, and John D. Chodera.
Proc. Natl. Acad. Sci. USA, 108:E1009 (2011) DOI: 10.1073/pnas.1106094108

Multistate Bennett acceptance ratio (MBAR) method (Python)

[SimTK page]

A convenient Python toolkit for performing calculations with the multistate Bennett acceptance ratio (MBAR) method for the analysis of equilibrium molecular simulations and single-molecule experiments.

This code accompanies the paper:

Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts and John D. Chodera.
J. Chem. Phys. 129:124105 (2008) DOI: 10.1063/1.2978177

Automatic state decomposition code (Fortran90/95)

[SimTK page]

A toolkit for the automated decomposition of macromolecular conformation spaces into kinetically metastable regions for the construction of Markov state models of conformational dynamics. Parallelized using OpenM to run on multiple CPUs on shared-memory architectures.

This code accompanies the following paper:

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
John D. Chodera*, Nina Singhal*, William C. Swope, Vijay S. Pande, and Ken A. Dill.
* These authors contributed equally to the work.
J. Chem. Phys. 126(15):155101 (2007) DOI: 10.1063/1.2714538

This code is now deprecated. Please consider using MSMBuilder or EMMA.

PTWHAM (Fortran90/95)

[SimTK page]

A toolkit for the analysis of simulated and parallel tempering simulation data with the PTWHAM variant of the weighted histogram analysis method (WHAM).

This code accompanies the following paper:

Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
John D. Chodera, William C. Swope, Jed W. Pitera, Chaok Seok, and Ken A. Dill.
J. Chem. Theor. Comput. 3(1):26-41 (2007) DOI: 10.1021/ct0502864

[Supplementary material (original F95 code)]

This code is now deprecated, having been replaced by the superior and simpler MBAR method.

Experimental data analysis tools

Single-molecule committor analysis for assessment of putative reaction coordinate quality (Matlab)

[SimTK page]

A set of Matlab scripts to analyze single-molecule experimental data to determine the quality of putative reaction coordinates by computing the committor (also known as the splitting probability or Pfold).

This code accompanies the paper:

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
John D. Chodera and Vijay S. Pande.
Phys. Rev. Lett., 107:098102 (2011) DOI: 10.1103/PhysRevLett.107.098102

Multistate Bennett acceptance ratio (MBAR) method (Python)

[SimTK page]

This code accompanies the paper:

Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts and John D. Chodera.
J. Chem. Phys. 129:124105 (2008) DOI: 10.1063/1.2978177

Bayesian hidden Markov models (BHMM) for single-molecule force spectroscopy (Matlab)

[SimTK page]

A Matlab toolkit for the analysis of equilibrium single-molecule force spectroscopy data with Bayesian hidden Markov models to estimate rate constants and characterize states.

This code accompanies the paper:

Bayesian hidden Markov model analysis of single-molecule biophysical experimens: Characterizing metastable states and transition rates under measurement uncertainty
John D. Chodera, Phillip Elms, Frank Noé, Bettina Keller, Christian M. Kaiser, Aaron Ewall-Wice, Susan Marqusee, Carlos J. Bustamante, and Nina Singhal Hinrichs.
arXiv: 1108.1430

Bayesian analysis of isothermal titration calorimetry (ITC) data (Python)

[SimTK page]

A Python toolkit for the automated analysis and design of isothermal titration calorimetry (ITC) experiments with Bayesian techniques. This procedure produces a much more accurate estimate of the true error characterizing the extracted thermodynamic parameters, including concentration errors, and provides joint probability distributions and confidence intervals for all estimated parameters. In addition, optimal Bayesian experimental design allows the design of ITC protocols that maximize information gain given initial data or guesses.

This paper accompanying this code is currently in preparation.

A robust approach to estimating rate constants from single-molecule experiments (Matlab)

[SimTK page]

Matlab scripts for computing robust estimates of rate constants from single-molecule (or simulation) data using time-correlation functions rather than counting transitions across a threshold.

This code accompanies the paper:

A robust approach to estimating rates from time-correlation functions
John D. Chodera Phillip J. Elms, William C. Swope, Jan-Hendrik Prinz, Susan Marqusee, Carlos Bustamante, Frank Noé, and Vijay S. Pande.
arXiv: 1108.2304

Datasets

Alanine dipeptide equilibrium simulation data (AMBER)

[SimTK page]

An extensive dataset of simulation data of the alanine dipeptide in explicit solvent using the AMBER96 forcefield and TIP3P water, in AMBER text coordinate trajectory format.

This code accompanies the paper:

jchodera@berkeley.edu · Last Modified 27 Nov 2011