Markov state models of protein misfolding

Protein Misfolding in Drosophila Models of Prionopathies

Situated State Hidden Markov Models

We introduce a probabilistic model called a Situated State Hidden Markov Model (SSHMM), in which states arèsituated' (i.e. assigned positions) and assumed to correspond to regions of an underlying continuous state space. Transition probabilities among states are induced by the assigned state positions in such a way that transitions occur more frequently between nearby states. The model is forma...

Markov state models of biomolecular conformational dynamics.

It has recently become practical to construct Markov state models (MSMs) that reproduce the long-time statistical conformational dynamics of biomolecules using data from molecular dynamics simulations. MSMs can predict both stationary and kinetic quantities on long timescales (e.g. milliseconds) using a set of atomistic molecular dynamics simulations that are individually much shorter, thus add...

Protein misfolding and neurodegeneration.

A key molecular pathway implicated in diverse neurodegenerative diseases is the misfolding, aggregation, and accumulation of proteins in the brain. Compelling evidence strongly supports the hypothesis that accumulation of misfolded proteins leads to synaptic dysfunction, neuronal apoptosis, brain damage, and disease. However, the mechanism by which protein misfolding and aggregation trigger neu...

Classification of Protein Sequences Using Markov Models Classification of Protein Sequences Using Markov Models

Preface This study was completed as a master thesis at the institute of Informatics and Mathematical Modeling (IMM)-Technical University of Denmark (DTU). The project has been completed in the period between September 1 st 2003 and Marts 1 st 2004 (and is rated as 35 points). Associate Professor Paul Fischer also IMM, DTU has been supervisor for the project. The report deals with a general clas...