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How scaffold proteins control information flow in signaling pathways is poorly understood: Do they simply tether components, or do they precisely orient and activate them? We found that the yeast mitogen-activated protein (MAP) kinase scaffold Ste5 is tolerant to major stereochemical perturbations; heterologous protein interactions could functionally replace native kinase recruitment interactions, indicating that simple tethering is largely sufficient for scaffold-mediated signaling. Moreover, b

Simulated tempering is a method to enhance simulations of complex systems by periodically raising and lowering the temperature. Despite its advantages, simulated tempering has been overshadowed by its parallel counterpart, replica exchange (also known as parallel tempering), due to the difficulty of weight determination in simulated tempering. Here we propose a simple and fast method to obtain near-optimal weights for simulated tempering, and demonstrate its effectiveness in a molecular dynamics

Article Share on Segment-based approach for subsequence searches in sequence databases Authors: Sanghyun Park Department of Computer Science, University of California, Los, Angeles, Los Angeles, CA Department of Computer Science, University of California, Los, Angeles, Los Angeles, CAView Profile , Sang-Wook Kim Department of Computer, Information, and Communications Engineering, Kangwon National University, Korea Department of Computer, Information, and Communications Engineering, Kangwon Natio

Finding representative reaction pathways is important for understanding the mechanism of molecular processes. We propose a new approach for constructing reaction paths based on mean first-passage times. This approach incorporates information about all possible reaction events as well as the effect of temperature. As an application of this method, we study representative pathways of excitation migration in a photosynthetic light-harvesting complex, photosystem I. The paths thus computed provide a

In the social ecological model, personal characteristics are important determinants of health behaviors, however, multi-dimensional approaches that consider social and physical environments must be utilized to gain a broader picture. Accordingly, this study examines the effects of personal, social, and physical environment variables as factors affecting levels of physical activity (METs). Our findings are based on 72,916 responses from the 2015 Community Health Survey in South Korea. Individual

Identifying alternative indications for known drugs is important for the pharmaceutical industry. Many computational methods have been proposed for predicting unknown associations between drugs and target proteins associated with diseases. To produce better prediction, researchers should not only develop accurate algorithms but identify good features that reflect intracellular systems. In this paper, we proposed a novel method for exploiting protein localization. We generated localization vector

Markov state models are kinetic models built from the dynamics of molecular simulation trajectories by grouping similar configurations into states and examining the transition probabilities between states. Here we present a procedure for validating the underlying Markov assumption in Markov state models based on information theory using Shannon's entropy. This entropy method is applied to a simple system and is compared with the previous eigenvalue method. The entropy method also provides a way