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CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to(More)
Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software.(More)
—Analytical compact-form models for the signal tran-sients and crosstalk noise of inductive-effect-prominent multi-coupled lines are developed. Capacitive and inductive coupling effects are investigated and formulated in terms of the effective single-transmission-line model and effective transmission line parameters for fundamental switching modes.(More)
<i>Background:</i> Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned(More)
Solid-state NMR (SSNMR) is an invaluable tool for determining orientations of membrane proteins and peptides in lipid bilayers. Such orientational descriptions provide essential information about membrane protein functions. However, when a semi-static single conformer model is used to interpret various SSNMR observables, important dynamics information can(More)
A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter(More)
Finding related articles from the PubMed (a large biomedical literature repository) is challenging because it is hard to express the user's specific relevance in the given query interface and a keyword query typically retrieves many results. Biomedical researchers spend a critical amount of time (e.g., often more than several days) in the literature search(More)