markov state models (Molecular Dynamics Inc)
86
Structured Review
Molecular Dynamics Inc
markov state models
Markov State Models, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/markov+state+model/markov+models+state/pm42301231-1092-19-16
Average 86 stars, based on 1 article reviews
Markov State Models, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/markov+state+model/markov+models+state/pm42301231-1092-19-16
Average 86 stars, based on 1 article reviews
markov state models - by Bioz Stars,
2026-09
86/100 stars
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other:Article Title: Evaluation and optimization of discrete state models of protein folding. Article Snippet: The space accessed by a folding macromolecule is vast, and how to best project computer simulations of protein folding trajectories into an interpretable sequence of discrete states is an open research problem.. There are numerous alternative ways of associating individual configurations into collective states, and in deciding on the number of such clustered states there is a trade-off between human interpretability (smaller number of states) and accuracy of representation (larger number of states).. Here we introduce a trajectory likelihood measure for assessing alternative discrete state models of protein folding. Article Title: Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics. Article Snippet: Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes, and has become routine thanks to increasingly powerful computational resources.. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena.. We present a unified framework called “Solvent-Shells Featurization” for including solvent degrees of freedom in analysis, and show that this method produces better models. Article Title: Comparative Analyses of the Conformational Dynamics Between the Soluble and Membrane-Bound Cytokine Receptors Article Snippet: Interleukin 1 family, Interleukin 1 receptor type 1, Interleukin 1 receptor like 1, ST2, IL-33, soluble cytokine receptor, Article Title: AutoGraph: Autonomous Graph-Based Clustering of Small-Molecule Conformations. Article Snippet: While accurately modeling the conformational ensemble is required for predicting properties of flexible molecules, the optimal method of obtaining the conformational ensemble appears as varied as their applications.. Ensemble structures have been modeled by generation, refinement, and clustering of conformations with a sufficient number of samples.. We present a conformational clustering algorithm intended to automate the conformational clustering step through the Louvain algorithm, which requires minimal hyperparameters and importantly no predefined number of clusters or threshold values. Comparison:Article Title: Structural Disorder of Folded Proteins: Isotope-Edited 2D IR Spectroscopy and Markov State Modeling Article Snippet: .. As a basis for characterizing structural heterogeneity, we make use of a Selection:Article Title: Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus. Article Snippet: .. Free energy profiles for wild-type FlhAC and FlhAC(G368C) at 27 C and 42 C were calculated as a function of the inter-domain distance between domain 2 and 4, d24, by the combination of the Parallel Cascade Selection Molecular Dynamics (PaCS-MD) (Harada and Kitao, 2013) and |