#### Filter Results:

- Full text PDF available (8)

#### Publication Year

2012

2017

- This year (1)
- Last 5 years (12)
- Last 10 years (12)

#### Publication Type

#### Co-author

#### Journals and Conferences

#### Data Set Used

#### Key Phrases

Learn More

- Rami Al-Rfou', Guillaume Alain, +109 authors Ying Zhang
- ArXiv
- 2016

Theano is a Python library that allows to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Since its introduction, it has been one of the most used CPU and GPU mathematical compilers - especially in the machine learning community - and has shown steady performance improvements. Theano is being actively… (More)

- Kyle A Beauchamp, Robert McGibbon, Yu-Shan Lin, Vijay S Pande
- Proceedings of the National Academy of Sciences…
- 2012

Markov state models constructed from molecular dynamics simulations have recently shown success at modeling protein folding kinetics. Here we introduce two methods, flux PCCA+ (FPCCA+) and sliding constraint rate estimation (SCRE), that allow accurate rate models from protein folding simulations. We apply these techniques to fourteen massive simulation… (More)

- Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu, Vijay S. Pande, Todd J. Martínez
- Nature chemistry
- 2014

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the… (More)

- Robert T McGibbon, Vijay S Pande
- The Journal of chemical physics
- 2015

Markov state models are a widely used method for approximating the eigenspectrum of the molecular dynamics propagator, yielding insight into the long-timescale statistical kinetics and slow dynamical modes of biomolecular systems. However, the lack of a unified theoretical framework for choosing between alternative models has hampered progress, especially… (More)

We present a machine learning framework for modeling protein dynamics. Our approach uses L1-regularized, reversible hidden Markov models to understand large protein datasets generated via molecular dynamics simulations. Our model is motivated by three design principles: (1) the requirement of massive scalability; (2) the need to adhere to relevant physical… (More)

- Robert T McGibbon, Brooke E Husic, Vijay S Pande
- The Journal of chemical physics
- 2017

Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems, as a maximally predictive one-dimensional projection. We then show that this criterion is uniquely satisfied by a… (More)

- Robert T McGibbon, Christian R Schwantes, Vijay S Pande
- The journal of physical chemistry. B
- 2014

Markov state models provide a powerful framework for the analysis of biomolecular conformation dynamics in terms of their metastable states and transition rates. These models provide both a quantitative and comprehensible description of the long-time scale dynamics of large molecular dynamics with a Master equation and have been successfully used to study… (More)

- C R Schwantes, R T McGibbon, V S Pande
- The Journal of chemical physics
- 2014

Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights.… (More)

- Robert T McGibbon, Vijay S Pande
- Journal of chemical theory and computation
- 2013

Statistical modeling of long timescale dynamics with Markov state models (MSMs) has been shown to be an effective strategy for building quantitative and qualitative insight into protein folding processes. Existing methodologies, however, rely on geometric clustering using distance metrics such as root mean square deviation (RMSD), assuming that geometric… (More)

- Lee-Ping Wang, Robert T McGibbon, Vijay S Pande, Todd J Martinez
- Journal of chemical theory and computation
- 2016

We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is… (More)