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1579 Publications visible to you, out of a total of 1579
Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions

Abstract

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Author: Max Waldhauer

Date Published: 2015

Publication Type: Bachelor's Thesis

Physically coherent probabilistic weather forecasts using multivariate discrete copula-based ensemble postprocessing methods

Abstract

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Author: Roman Schefzik

Date Published: 2015

Publication Type: Doctoral Thesis

A fast projection method for connectivity constraints in image segmentation

Abstract

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Authors: Jan Stühmer, Daniel Cremers

Date Published: 2015

Publication Type: InProceedings

Model-based tracking at 300hz using raw time-of-flight observations

Abstract

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Authors: Jan Stuhmer, Sebastian Nowozin, Andrew Fitzgibbon, Richard Szeliski, Travis Perry, Sunil Acharya, Daniel Cremers, Jamie Shotton

Date Published: 2015

Publication Type: InProceedings

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Abstract

Not specified

Authors: Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

Date Published: 1st Dec 2014

Publication Type: Journal

Mechanisms and Energetics of Potassium Channel Block by Local Anesthetics and Antifungal Agents

Abstract (Expand)

Many drug molecules inhibit the conduction of several families of cation channels by binding to a small cavity just below the selectivity filter of the channel protein. The exact mechanisms governing … drug–channel binding and the subsequent inhibition of conduction are not well understood. Here the inhibition of two K+ channel isoforms, Kv1.2 and KCa3.1, by two drug molecules, lidocaine and TRAM-34, is examined in atomic detail using molecular dynamics simulations. A conserved valine-alanine-valine motif in the inner cavity is found to be crucial for drug binding in both channels, consistent with previous studies of similar systems. Potential of mean force calculations show that lidocaine in its charged form creates an energy barrier of ∼6 kT for a permeating K+ ion when the ion is crossing over the drug, while the neutral form of lidocaine has no significant effect on the energetics of ion permeation. On the other hand, TRAM-34 in the neutral form is able to create a large energy barrier of ∼10 kT by causing the permeating ion to dehydrate. Our results suggest that TRAM-34 analogues that remain neutral and permeable to membranes under acidic conditions common to inflammation may act as possible drug scaffolds for combating local anesthetic failure in inflammation.

Authors: Rong Chen, Ganna Gryn’ova, Yingliang Wu, Michelle L. Coote, Shin-Ho Chung

Date Published: 24th Oct 2014

Publication Type: Journal

Macromolecular Entropy Can Be Accurately Computed from Force

Abstract (Expand)

A method is presented to evaluate a molecule’s entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix … produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a β hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The method’s accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.

Authors: Ulf Hensen, Frauke Gräter, Richard H. Henchman

Date Published: 15th Oct 2014

Publication Type: Journal

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