We propose an efficient method for the prediction of protein folding rate constants and mechanisms. We use molecular dynamics simulation data to build Markovian state models (MSMs), discrete representations of the pathways sampled. Using these MSMs, we can quickly calculate the folding probability (P(fold)) and mean first passage time of all the sampled points. In addition, we provide technique...

OBJECTIVES To measure potential acceptability of rectal microbicides and to explore factors likely to affect their acceptability among men who have sex with men (MSM). METHODS Cross-sectional and retrospective surveys were conducted in this study. A questionnaire and a scale were used to measure the acceptability score for physical and functional characteristics of hypothetical rectal microbi...

Markov state models (MSMs) have been successful in computing metastable states, slow relaxation timescales and associated structural changes, and stationary or kinetic experimental observables of complex molecules from large amounts of molecular dynamics simulation data. However, MSMs approximate the true dynamics by assuming a Markov chain on a clusters discretization of the state space. This ...

Robins (1993, 1994, 1997, 1998ab) has developed a set of causal or counterfactual models, the structural nested models (SNMs). This paper describes an alternative new class of causal modelsthe (non-nested) marginal structural models (MSMs). We will then describe a class of semiparametric estimators for the parameters of these new models under a sequential randomization (i.e., ignorability) assu...

Purpose This paper aims to investigate the pass-through (PT) effect in Turkey by using quarterly data for period 1998: Q1-2019: Q2 understand dynamic potential effects of exchange rates on domestic prices. Design/methodology/approach The launches several nonlinear models which basic determinants prices are determined through Markov regime-switching (MSMs). Hence, this research follows variables...

Part of understanding a molecule's conformational dynamics is mapping out the dominant metastable, or long lived, states that it occupies. Once identified, the rates for transitioning between these states may then be determined in order to create a complete model of the system's conformational dynamics. Here we describe the use of the MSMBuilder package (now available at http://simtk.org/home/m...

Multi-sided markets (MSMs) have proven to be a successful business model in the dynamic electronic commerce environment. There exists variety of MSMs differing their provided features and services for participants. Existing taxonomies often focus on value creation business-to-business transactions. We apply Nickerson et al.’s taxonomy development approach. especially incorporated aspects orches...

Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analytical representation of only the solvent-accessible surface. There are a few programs that compute the analytical representation of the solvent-excluded surface, but they often have problems handling sin...