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The SMART Cyberinfrastructure: Spa ce-Time Multiscale Approaches for Research and Technology
Published in Tanmoy Chakraborty, Prabhat Ranjan, Anand Pandey, Computational Chemistry Methodology in Structural Biology and Materials Sciences, 2017
Daniele Licari, Giordano Mancini, Andrea Brogni, Andrea Salvadori, Vincenzo Barone
As cited in the Introduction together with “computational engines” molecular graphics were developed since the birth of molecular modeling, evolving in a sort of extension of the “classical” chemical language [50]. Nowadays, many good software packages are available for interactive 3-D molecular graphics with focus one several areas of molecular modeling, including biochemistry and structural biology (e.g., VMD [51] or UCSF Chimera [52, 53, 54]), quantum chemistry (Molden, GaussView and ECCE [55]), and crystallography and material science (XCrysDen [56] and PLATON [57]). Many of them provide the ability to extend their functionality through scripts or plug-ins and in some cases may act as front-end for a computational software (e.g., GaussView for Gaussian or VMD [51] for NAMD [58]). The following list includes some of the most commons conventions used in modern molecular graphics to represent molecules and molecular properties, each one coupled with an example from Figure 5.9, obtained with the Caffeine molecular viewer [59].All-atoms models: atoms and bonds are represented by combinations of cylinders and spheres with different coloring, shading and dimensions according to their nature and/or to highlight some particular subset of atoms.“Ribbon” models: for large macromolecules, instead of drawing all the atoms it may be convenient to highlight a supramolecular structural motif (e.g., the DNA double helix) using continuous ribbon shaped lines; again color, size, shading and textures may be combined to convey several layer of information, in combination with all-atoms conventions.Isosurfaces and slicing planes: the property under investigation (e.g., Van der Waals surfaces, atomic orbitals, electrostatic potentials) is drawn using a particular isosurface to show, at a constant value, its distribution in three dimensional space or the average along one axis for a slicing plane. The featured property may convey further data employing color gradients.
Evaluation of a single amino acid substitution at position 79 of human IFN-α2b in interferon-receptor assembly and activity
Published in Preparative Biochemistry and Biotechnology, 2019
Samira Talebi, Alireza Saeedinia, Mehdi Zeinoddini, Fathollah Ahmadpour, Majid Sadeghizadeh
All structures were confirmed with server MDWEB (http://mmb.irbbarcelona.org/MDWeb). Besides, modeled protein structures were imagined by Molegro (ApS, DK-8000Aalhus C, Denmark) as a Virtual Docker and hydrogens were supplemented to structures by Chimera software (Molecular graphics and analyses performed with UCSF Chimera, developed by the Resource for Biocounting, Visualization, and informatics at the university of California, Sanferancisco, with support from NIH P41-GM103311). The structural resemblance and mutant were checked by the RMSD value calculation using VMD software.