Journal ArticleDOI
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.
Martin K. Scherer,Benjamin Trendelkamp-Schroer,Fabian Paul,Guillermo Pérez-Hernández,Moritz Hoffmann,Nuria Plattner,Christoph Wehmeyer,Jan-Hendrik Prinz,Frank Noé +8 more
TLDR
The open-source Python package PyEMMA is presented, derived a systematic and accurate way to coarse-grain MSMs to few states and to illustrate the structures of the metastable states of the system.Abstract:
Markov (state) models (MSMs) and related models of molecular kinetics have recently received a surge of interest as they can systematically reconcile simulation data from either a few long or many short simulations and allow us to analyze the essential metastable structures, thermodynamics, and kinetics of the molecular system under investigation. However, the estimation, validation, and analysis of such models is far from trivial and involves sophisticated and often numerically sensitive methods. In this work we present the open-source Python package PyEMMA (http://pyemma.org) that provides accurate and efficient algorithms for kinetic model construction. PyEMMA can read all common molecular dynamics data formats, helps in the selection of input features, provides easy access to dimension reduction algorithms such as principal component analysis (PCA) and time-lagged independent component analysis (TICA) and clustering algorithms such as k-means, and contains estimators for MSMs, hidden Markov models, an...read more
Citations
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Journal ArticleDOI
Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation.
Marek Wieczorek,Esam T. Abualrous,Jana Sticht,Miguel Álvaro-Benito,Sebastian Stolzenberg,Frank Noé,Christian Freund +6 more
TL;DR: Recent studies predict a high impact of protein intermediate states on MHC allele-specific peptide presentation, which implies a profound influence of MHC dynamics on the phenomenon of immunodominance and the development of autoimmune diseases.
Journal ArticleDOI
Markov State Models: From an Art to a Science
Brooke E. Husic,Vijay S. Pande +1 more
TL;DR: An overview of the MSM field to date is presented, presented for a general audience as a timeline of key developments in the field, and the current frontiers of methods development are highlighted, as well as exciting applications in experimental design and drug discovery.
Journal ArticleDOI
VAMPnets for deep learning of molecular kinetics.
TL;DR: A deep learning framework that automates construction of Markov state models from MD simulation data is introduced that performs equally or better than state-of-the-art Markov modeling methods and provides easily interpretable few-state kinetic models.
Journal ArticleDOI
Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning
TL;DR: Boltzmann generators are trained on the energy function of a many-body system and learn to provide unbiased, one-shot samples from its equilibrium state and can be trained to directly generate independent samples of low-energy structures of condensed-matter systems and protein molecules.
Journal ArticleDOI
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Jiří Šponer,Giovanni Bussi,Miroslav Krepl,Miroslav Krepl,Pavel Banáš,Sandro Bottaro,Richard A. Cunha,Alejandro Gil-Ley,Giovanni Pinamonti,Simón Poblete,Petr Jurečka,Nils G. Walter,Michal Otyepka +12 more
TL;DR: An in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods are covered.
References
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Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
A tutorial on hidden Markov models and selected applications in speech recognition
TL;DR: In this paper, the authors provide an overview of the basic theory of hidden Markov models (HMMs) as originated by L.E. Baum and T. Petrie (1966) and give practical details on methods of implementation of the theory along with a description of selected applications of HMMs to distinct problems in speech recognition.
Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.
Journal ArticleDOI
Least squares quantization in PCM
TL;DR: In this article, the authors derived necessary conditions for any finite number of quanta and associated quantization intervals of an optimum finite quantization scheme to achieve minimum average quantization noise power.