scholarly journals Improving Conformer Generation for Small Rings and Macrocycles Based on Distance Geometry and Experimental Torsional-Angle Preferences

2020 ◽  
Vol 60 (4) ◽  
pp. 2044-2058 ◽  
Author(s):  
Shuzhe Wang ◽  
Jagna Witek ◽  
Gregory A. Landrum ◽  
Sereina Riniker
Author(s):  
Shuzhe Wang ◽  
Kajo Krummenacher ◽  
Gregory A. Landrum ◽  
Benjamin D. Sellers ◽  
Paola Di Lello ◽  
...  

2020 ◽  
Author(s):  
Jeffrey Mendenhall ◽  
Benjamin Brown ◽  
Sandeepkumar Kothiwale ◽  
Jens Meiler

<div>This paper describes recent improvements made to the BCL::Conf rotamer generation algorithm and comparison of its performance against other freely available and commercial conformer generation software. We demonstrate that BCL::Conf, with the use of rotamers derived from the COD, more effectively recovers crystallographic ligand-binding conformations seen in the PDB than other commercial and freely available software. BCL::Conf is now distributed with the COD-derived rotamer library, free for academic use. The BCL can be downloaded at <a href="http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1">http://meilerlab.org/ bclcommons</a> for Windows, Linux, or Apple operating systems.<br></div>


Algorithmica ◽  
2021 ◽  
Author(s):  
Douglas S. Gonçalves ◽  
Carlile Lavor ◽  
Leo Liberti ◽  
Michael Souza

2021 ◽  
Vol 34 (1) ◽  
Author(s):  
Maoqing Xie ◽  
Leigang Wang ◽  
Yao Huang

AbstractThe clutch is an important component of the vehicle driveline system. One of its major functions is to attenuate or eliminate the torsional vibration and noise of the driveline system caused by the engine. Based on experiments of vibration damping under different vehicle conditions, the structure and functional principle of a clutch-driven disc assembly for a wide-angle, large-hysteresis, multistage damper is investigated in this study using an innovative combined approach. Furthermore, a systematic integration of key technologies, including wide-angle low-stiffness damping technology, large-hysteresis clutch technology, a novel split pre-damping structure technology, damping structure technology for component cushioning, and multistage damping structure technology, is proposed. The results show that the total torsional angle of the wide-angle large-hysteresis, multistage damper is more than twice that of the traditional clutch damper. The multistage damping design allows a better consideration of various damping requirements under different vehicle conditions, which can effectively address problems of severe idle vibrations and torsional resonance that occur under idled and accelerated conditions. Meanwhile, the use of a large-hysteresis structure and wear-resistant materials not only improves the vibration damping performance, but also prolongs the product service life, consequently resulting in multi-faceted optimization and innovative products.


Author(s):  
Phil Duxbury ◽  
Carlile Lavor ◽  
Leo Liberti ◽  
Luiz Leduino de Salles-Neto

Author(s):  
Maurizio Bruglieri ◽  
Roberto Cordone ◽  
Leo Liberti
Keyword(s):  

2021 ◽  
Vol 75 (1) ◽  
pp. 39-70
Author(s):  
Lorna J. Smith ◽  
Wilfred F. van Gunsteren ◽  
Bartosz Stankiewicz ◽  
Niels Hansen

AbstractValues of 3J-couplings as obtained from NMR experiments on proteins cannot easily be used to determine protein structure due to the difficulty of accounting for the high sensitivity of intermediate 3J-coupling values (4–8 Hz) to the averaging period that must cover the conformational variability of the torsional angle related to the 3J-coupling, and due to the difficulty of handling the multiple-valued character of the inverse Karplus relation between torsional angle and 3J-coupling. Both problems can be solved by using 3J-coupling time-averaging local-elevation restraining MD simulation. Application to the protein hen egg white lysozyme using 213 backbone and side-chain 3J-coupling restraints shows that a conformational ensemble compatible with the experimental data can be obtained using this technique, and that accounting for averaging and the ability of the algorithm to escape from local minima for the torsional angle induced by the Karplus relation, are essential for a comprehensive use of 3J-coupling data in protein structure determination.


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