Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case

2014 ◽  
Vol 16 (27) ◽  
pp. 14047-14058 ◽  
Author(s):  
Francisco Adasme-Carreño ◽  
Camila Muñoz-Gutierrez ◽  
Julio Caballero ◽  
Jans H. Alzate-Morales
Keyword(s):  
Hydrogen Bond ◽  
Protein Kinase ◽  
Network Analysis ◽  
Binding Site ◽  
Case Studies ◽  
Hydrogen Bond Network ◽  
Frame Selection ◽  
Bond Network

Conformational clustering using hydrogen bond network analysis improved the MM/GBSA scoring for some protein-kinase–ligand systems used as case studies.

Effect of the hydrogen bond network in carbonic anhydrase II zinc binding site. A theoretical study

1998 ◽  
Vol 76 (7) ◽  
pp. 1027-1032 ◽  
Author(s):  
Silvia Álvarez-Santos ◽  
Àngels González-Lafont ◽  
José M Lluch
Keyword(s):  
Hydrogen Bond ◽  
Carbonic Anhydrase ◽  
Binding Site ◽  
Zinc Binding ◽  
Carbonic Anhydrase Ii ◽  
Am1 Method ◽  
Hydrogen Bond Network ◽  
Zinc Binding Site ◽  
Bond Network ◽  
Metal Ligand

The hydrogen bond network influence on the carbonic anhydrase II (CAII) zinc binding site has been studied theoretically by using the semiempirical AM1 method. To this aim, quantum mechanical reduced models of wild-type CAII and several CAII variants have been constructed. We have shown that, when a direct metal ligand donates a hydrogen bond to an indirect metal ligand, the first-shell residues enhance their electrostatic interaction with the zinc cation. Thus, the hydrogen-bond network is able to modulate the zinc binding affinity and the zinc-water pKa.Key words: hydrogen bond network, carbonic anhydrase II, Zn2+ metalloenzyme ligands.

How does hydrogen bond network analysis reveal the golden ratio of water–glycerol mixtures?

2020 ◽  
Vol 22 (5) ◽  
pp. 2887-2907
Author(s):  
Trevor R. Fisher ◽  
Guobing Zhou ◽  
Yijun Shi ◽  
Liangliang Huang
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Network Analysis ◽  
Molecular Dynamics Simulations ◽  
Golden Ratio ◽  
Hydrogen Bond Network ◽  
Maximum Contribution ◽  
Water Glycerol ◽  
Bond Network ◽  
Dynamics Simulations

Molecular dynamics simulations reveal that the maximum contribution of H-bonds between water and glycerol occurs around 30 mol% glycerol. Such a concentration is also where several of the mixture's properties have an observed maxima or minima.

scholarly journals Evidence for an Extended Hydrogen Bond Network in the Binding Site of the Nicotinic Receptor

2011 ◽  
Vol 286 (37) ◽  
pp. 32251-32258 ◽  
Author(s):  
Angela P. Blum ◽  
Kristin Rule Gleitsman ◽  
Henry A. Lester ◽  
Dennis A. Dougherty
Keyword(s):  
Hydrogen Bond ◽  
Binding Site ◽  
Nicotinic Receptor ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I

2020 ◽  
Vol 1861 (10) ◽  
pp. 148240 ◽  
Author(s):  
Umesh Khaniya ◽  
Chitrak Gupta ◽  
Xiuhong Cai ◽  
Junjun Mao ◽  
Divya Kaur ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Network Analysis ◽  
Proton Transfer ◽  
Complex I ◽  
Hydrogen Bond Network ◽  
Bond Network

Water phase transitions from the perspective of hydrogen-bond network analysis

2018 ◽  
Vol 20 (44) ◽  
pp. 28308-28318 ◽  
Author(s):  
B. V. Ramírez ◽  
R. M. Benito ◽  
J. Torres-Arenas ◽  
A. L. Benavides
Keyword(s):  
Hydrogen Bond ◽  
Phase Transitions ◽  
Network Analysis ◽  
Water Phase ◽  
Hydrogen Bond Network ◽  
Hydrogen Bond Networks ◽  
Bond Network

Analysis of the water phase transitions from the perspective of hydrogen bond networks.

Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

2021 ◽  
pp. 120431
Author(s):  
Akinori Honda ◽  
Shunta Kakihara ◽  
Shuhei Ichimura ◽  
Kazuaki Tomono ◽  
Mina Matsushita ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Kinetics ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Kinetics Of
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