Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules

Arroyuelo, Agustina; Vila, Jorge A.; Martin, Osvaldo A.

doi:10.1007/s10822-016-9944-x

Cited by 23 publications

(18 citation statements)

References 26 publications

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“…Free web-tools, such as GLYCAM-Web, CHARMM-GUI, POLYS glycan builder, GAG-builder, SWEET-II should be noted (more references are listed in Table 2 ). A few commercial molecular modeling software is equipped with special plugins for glycan 3D structure building based on a list of predefined monosaccharide templates, e.g., Sugar Builder tool in HyperChem ( ) software [ 346 ] or Azahar [ 235 ] plugin in PyMol package (Schrödinger software) ( )[ 347 ].…”

Section: 3d Structure Input and Visualizationmentioning

confidence: 99%

See 1 more Smart Citation

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Scherbinina

Toukach

2020

IJMS

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Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

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Section: 3d Structure Input and Visualizationmentioning

confidence: 99%

“…Another UnityMol visualization approach called Umbrella Visualization [ 363 , 364 ] was tailored for N-glycan structures. Azahar plugin for PyMol [ 235 ] affords cartoon models with polygons and rods. Several solutions for convenient visualization came up with the development of SNFG notation [ 339 ].…”

Section: 3d Structure Input and Visualizationmentioning

confidence: 99%

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Scherbinina

Toukach

2020

IJMS

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“…PyMOL includes a plugin called Azahar [32] which is able to build a glycan from a template list of saccharide structures. The plugin adds three specific display modes aimed at simplifying the representation of glycan structures: the cartoon and wire representations show the cycles as non-flat polygons linked by rods and the bead representation shows each cycle as a sphere.…”

Section: Visualizationmentioning

confidence: 99%

Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol

Besancon

Guillot

Blaise

et al. 2020

Methods

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A B S T R A C TN-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of Nglycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions. Thr and Asn-X-Ser, where X is any amino acid but not proline [10]. In

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“…In the resulting 200 conformational combinations, the best binding conformation was selected based on the reasonable binding site and the minimum binding free energy. PyMOL and Discovery Studio 4.5 programs were acquired on analysis and drawing for the molecular docking . The binding free energy of the CphA‐antibiotic complex was calculated using the molecular force field method …”

Section: Materials and Proceduresmentioning

confidence: 99%

“…Then, the system was heated drawing for the molecular docking. 19,20 The binding free energy of the CphA-antibiotic complex was calculated using the molecular force field method. [21][22][23] 3 | RESULTS AND DISCUSSION 3.1 | Expression and activity of CphA…”

Section: Molecular Simulationmentioning

confidence: 99%

Recognition and interaction of CphA from Aeromonas hydrophila with imipenem and biapenem by spectroscopic analysis in combination with molecular docking

Zhang

Bian

2019

J of Molecular Recognition

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The molecular recognition and interaction of CphA from Aeromonas hydrophila with imipenem (Imip) and biapenem (Biap) were studied by means of the combined use of fluorescence spectra and molecular docking. The results showed that both the fluorescence quenching of CphA by Imip and Biap were caused through the combined dynamic and static quenching, and the latter was dominating in the process; the microenvironment and conformational of CphA were altered upon the addition of Imip and Biap from synchronous and three‐dimensional fluorescence. The binding of CphA with Imip or Biap caused a conformational change in the loop of CphA, and through the conformational change, the loop opened the binding pocket of CphA to allow for an induced fit of the newly introduced ligand. In the binding of CphA with Imip, the whole molecule entered into the active pocket of CphA. The binding was driven by enthalpy change, and the binding force between them was mainly hydrogen bonding and Van der Waals force; whereas in the binding of CphA with Biap, only the beta‐lactam ring of Biap entered into the binding pocket of CphA while the side chain was located outside the active pocket. The binding was driven by the enthalpy change and entropy change together, and the binding force between them was mainly electrostatic interaction. This study provided an insight into the recognition and binding of CphA with antibiotics, which may be helpful for designing new substrate for beta‐lactamase and developing new antibiotics resistant to superbugs.

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Azahar: a PyMOL plugin for construction, visualization and analysis of glycan molecules

Cited by 23 publications

References 26 publications

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Three-Dimensional Structures of Carbohydrates and Where to Find Them

Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol

Recognition and interaction of CphA from Aeromonas hydrophila with imipenem and biapenem by spectroscopic analysis in combination with molecular docking

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