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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

Properties of optically selected BL Lacertae candidates from the SDSS

Abstract (Expand)

Context. Deep optical surveys open the avenue for finding large numbers of BL Lac objects that are hard to identify because they lack the unique properties classifying them as such. While radio or X-ray …ay surveys typically reveal dozens of sources, recent compilations based on optical criteria alone have increased the number of BL Lac candidates considerably. However, these compilations are subject to biases and may contain a substantial number of contaminating sources. Aims. In this paper we extend our analysis of 182 optically selected BL Lac object candidates from the SDSS with respect to an earlier study. The main goal is to determine the number of bona fide BL Lac objects in this sample. Methods. We examine their variability characteristics, determine their broad-band radio-UV spectral energy distributions (SEDs), and search for the presence of a host galaxy. In addition we present new optical spectra for 27 targets with improved signal-to-noise ratio with respect to the SDSS spectra. Results. At least 59% of our targets have shown variability between SDSS DR2 and our observations by more than 0.1–0.27 mag depending on the telescope used. A host galaxy was detected in 36% of our targets. The host galaxy type and luminosities are consistent with earlier studies of BL Lac host galaxies. Simple fits to broad-band SEDs for 104 targets of our sample derived synchrotron peak frequencies between 13.5 ≤ log 10(νpeak) ≤ 16 with a peak at log 10 ~ 14.5. Our new optical spectra do not reveal any new redshift for any of our objects. Thus the sample contains a large number of bona fide BL Lac objects and seems to contain a substantial fraction of intermediate-frequency peaked BL Lacs.

Authors: S. D. Kügler, K. Nilsson, J. Heidt, J. Esser, T. Schultz

Date Published: 1st Sep 2014

Publication Type: Journal

On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics

Abstract

Not specified

Authors: Jonathan C. Fuller, Michael Martinez, Rebecca C. Wade

Date Published: 20th Aug 2014

Publication Type: Journal

Drug Metabolism Prediction

Abstract

Not specified

Authors: Ghulam Mustafa, Xiaofeng Yu, Rebecca C. Wade

Date Published: 11th Jul 2014

Publication Type: InBook

Data extraction for the reaction kinetics database SABIO-RK

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting … the computational modeling to create models of biochemical reaction networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications. Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner.

Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

Date Published: 1st May 2014

Publication Type: Journal

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