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Bendix: intuitive helix geometry analysis and abstraction

A. C. E. Dahl, M. Chavent, M. S. P. Sansom
2012 Bioinformatics  
Software is presented that quantifies and projects the helix axis evolution over time, with the choice of uniform or analytic heatmap graphics according to the local geometry.  ...  The flexibility of α-helices is important for membrane protein function and calls for better visualization and analysis.  ...  We thank Oliver Beckstein, Philip Fowler, Sarah Rouse and Ben Hall for suggesting features and testing the software.  ... 
doi:10.1093/bioinformatics/bts357 pmid:22730430 pmcid:PMC3413393 fatcat:geqzooy5nbdutpl37tfb5v6kcy

Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels

Michael Bründl, Sarala Pellikan, Anna Stary-Weinzinger
2021 Frontiers in Molecular Biosciences  
Dysfunction is linked to neonatal diabetes and other diseases.  ...  K+ flux through these channels is controlled by conformational changes in the helix bundle region, which acts as a physical barrier for K+ permeation.  ...  E., Chavent, M., and Sansom, M. S. P. (2012). Bendix: Intuitive Helix Geometry Analysis and Abstraction.  ... 
doi:10.3389/fmolb.2021.711975 pmid:34447786 pmcid:PMC8384051 fatcat:pfvosekc6vbljos6tzhehqtogu

Serpin latency transition at atomic resolution

G. Cazzolli, F. Wang, S. a Beccara, A. Gershenson, P. Faccioli, P. L. Wintrode
2014 Proceedings of the National Academy of Sciences of the United States of America  
Changes to the helix start and end altered the value of the angles but not the trend.1. Dahl ACE, Chavent M, Sansom MSP (2012) Bendix: Intuitive helix geometry analysis and abstraction.  ...  Kink angles were calculated along the DRP trajectories using Bendix (1).  ... 
doi:10.1073/pnas.1407528111 pmid:25313058 pmcid:PMC4217474 fatcat:vsigbos5rbhn5ioutxv5tgnlke

Elucidating the Structural Features of ABCA1 in its Heterogeneous Membrane Environment

S. Sunidhi, Sukriti Sacher, Atul, Parth Garg, Arjun Ray
2022 Frontiers in Molecular Biosciences  
This is followed by sequestration via a direct interaction between ABCA1 and its partner, ApoA1.  ...  ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis.  ...  Bendix: Intuitive helix Geometry Analysis and Abstraction.  ... 
doi:10.3389/fmolb.2021.803078 pmid:35155567 pmcid:PMC8830745 fatcat:ulgan2wrzvhujpon2fperqlhry

Structure of bacterial phospholipid transporter MlaFEDB with substrate bound

Nicolas Coudray, Georgia L Isom, Mark R MacRae, Mariyah N Saiduddin, Gira Bhabha, Damian C Ekiert
2020 eLife  
An MCE transport system called Mla has been implicated in phospholipid trafficking and outer membrane integrity, and includes an ABC transporter, MlaFEDB.  ...  Our structure provides mechanistic insight into substrate recognition and transport by MlaFEDB.  ...  P. (2012) 'Bendix: intuitive helix geometry 537 analysis and abstraction', Bioinformatics , 28(16), pp. 2193-2194. 538 Echols, N. et al. (2012) 'Graphical tools for macromolecular crystallography in PHENIX  ... 
doi:10.7554/elife.62518 pmid:33236984 pmcid:PMC7790496 fatcat:ere64lnax5e5xohceutyfpx3xy

Uncertainty-aware visualization techniques [article]

Christoph Schulz, Universität Stuttgart
Whether and how we present this uncertainty can have a major impact on how our audience perceives such information. Still, uncertainty is rarely visualized and communicated.  ...  The focus lies on modeling, propagation, and visualization of uncertainty. As encodings of uncertainty, we propose wave-like splines and sampling-based transparency.  ...  For example, VMD offers the option to depict helices as thick, straight cylinders encompassing the whole helix or as thick tubes that follow the centerline of the helix (Bendix representation [DCS12]  ... 
doi:10.18419/opus-12115 fatcat:la56gcmgkjgd3kyr45muwqnide

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
The authors are also thankful to Biobyte Corp. and Dr Hansch and Dr Leo for their support and free access to the C-QSAR program.  ...  , Nature Conservation and Nuclear Safety.  ...  A frequency analysis was carried out for each optimized geometry.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

[Back cover]

1962 IRE Transactions on Antennas and Propagation  
i These abstracts are reprinted as a service to readers of the journal and may not be cited as l I a reference to the TRIXSACTIOSS.  ...  Because of the geometry, use of vertical linear radiators is indicated.  ...  He then joined the Bendix Radio Division, Bendix Corporation, where he was engaged in the development of antenna and microwave components and systems.  ... 
doi:10.1109/tap.1962.1137902 fatcat:c7f6kvxiszhtnbf2tfyd3xhj6i

Protein crowding mediates membrane remodeling in upstream ESCRT-induced formation of intraluminal vesicles

Susanne Liese, Eva Maria Wenzel, Ingrid Kjos, Rossana Rojas Molina, Sebastian W. Schultz, Andreas Brech, Harald Stenmark, Camilla Raiborg, Andreas Carlson
2020 Proceedings of the National Academy of Sciences of the United States of America  
Combining experimental measurements and electron microscopy analysis of ESCRT-III–depleted cells with a mathematical model, we show that upstream ESCRT-induced alteration of the Gaussian bending rigidity  ...  and their crowding in concert with the transmembrane cargo on the membrane induce membrane deformation and facilitate ILV formation: Upstream ESCRT-driven budding does not require ATP consumption as only  ...  Non-dimensional analysis A usual step of analysis consists in finding the dimensionless form of both the shape equations and the boundary conditions.  ... 
doi:10.1073/pnas.2014228117 pmid:33139578 fatcat:fczwkdsn3zck3fuhejtiyzplka

Critical GIS : theorizing an emerging science

Nadine Cato Schuurman
The first section begins with an analysis of the bases and motivation of external assessments of GIS.  ...  A re-analysis of critiques, from the perspectives of GIS practitioners, investigates objections to critical accounts of the technology.  ...  To take an example, the kinds of methods of spatial analysis that we were developing in the late 70s and early 80s represented by geomathematical analysis were becoming very abstract and abstruse.  ... 
doi:10.14288/1.0089782 fatcat:dqzx5ut5nzhxpiqixd3jxdca4u

Lunar heat-flow experiment : final technical report

Marcus G Langseth, Stephen J Keihm
Bilson and M. Yerbury (1973) Grain size analysis and high frequency electrical properties of Apollo 15 and 16 samples (abstract) in. Lunar Science IV, p. 293-295.  ...  Little, Texas Instruments, Bendix and Teledyne Corporation.  ...  Tests of this bit were successful, giving rates of 4 inches/minute in vesi¬ cular basalt and 1 inch/minute in dense basalt.  ... 
doi:10.7916/d8-5t4m-3713 fatcat:p43alv2hznhsfhfp6kvo2gecda

Robotic isotropy and optimal robot design of planar manipulators

M.V. Kircanski
Proceedings of the 1994 IEEE International Conference on Robotics and Automation  
Standard bendix drive. Compression spring bendix drive overrunning clutch drive. Starter motor solenoids and switches. LIGHTING Lighting system wiring circuit.  ...  b) Component Analysis: Geometry, accuracy, material, machinability, quantity, modifications so as to assist production.  ...  , Spatial autocorrelation, Quadrat counts and Nearest-Neighbor analysis, Trend surface analysis, Gravity models. 7.  ... 
doi:10.1109/robot.1994.351213 dblp:conf/icra/Kircanski94 fatcat:uawqnzropbgivcanzqihtimt2m