MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

By Kyle A. Beauchamp, Gregory R. Bowman, T. J. Lane, L. Maibaum, I. Haque, Vijay S. Pande. Journal of Chemical Theory and Computation, 2011

380 citations recorded by the source corpus.

Markov State Models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov State Models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/65aaf814b43994af4bb920982a2c496a011cb4a0

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Frank No'e
2. Cecilia Clementi
3. Hao Wu
4. Vijay S. Pande
5. G. de Fabritiis
6. Xuhui Huang
7. Siqin Cao
8. Wei Wang

In Spectroscopy

1. Frank No'e
2. Cecilia Clementi
3. Xuhui Huang
4. Siqin Cao
5. Wei Wang
6. Lizhe Zhu
7. G. de Fabritiis
8. Vijay S. Pande

Citations in the corpus

• Kinetic distance and kinetic maps from molecular dynamics simulation. (2015, methodology): “ to the true eigenfunctions, it canbedirectlyappliedtomoleculardynamicsdata,requiresfewmodelingdecisionstobemade,andis readilyavailableintheMarkovmodelingpackagesEMMA[32](www.pyemma.org)andMSMbuilder [4]. Using the TICA eigenvalues and eigenvectors we employ the kinetic distance as a distance metric”
• Constructing Markov State Models to elucidate the functional conformational changes of complex biomolecules (2018, methodology): “The simplest way to impose detailed balance is to directly symmetrize the TCM by adding its transpose Csym τð Þ = C τð Þ+CT τð Þ =2 ð10Þ Volume 8, January/February 2018 © 2017 Wiley Per iodica ls , Inc. 7 of 18 before normalization.65 As the direct symmetrization is not a good approximation when the”
• Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways (2013, methodology): “In between rounds, each set of trajectories was sampled at 0.5 ns and clustered according to the MSM criteria described below into 1000 microstates with MSMBuilder 2 (36) from which new starting structures were chosen uniformly for the next round.”
• Identification of slow molecular order parameters for Markov model construction. (2013, methodology): “For clustering and Markov model construction of molecular dynamics data, the packages EMMA [83], MSMbuilder [5], Wordom [82] and METAGUI [8] are currently available.”