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Statistical Reconstruction and Heterogeneity Characterization in 3-D Biological Macromolecular Complexes
Published in Jeffrey P. Simmons, Lawrence F. Drummy, Charles A. Bouman, Marc De Graef, Statistical Methods for Materials Science, 2019
A key part of the x-ray crystallographic structure of FHV is that a part of the RNA genome of the particle can be seen in the structure as a dodecahedral cage just below the protein shell (“capsid”) of the structure. After removing the capsid by using the UCSF Chimera [781] visualization software, we also can see the dodecahedral cage as a low variance (blue color) region in Figure 7.2(d). Thus we both confirm the x-ray crystallographic result and increase our confidence in the meaningful nature of our variance maps.
Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants
Published in Journal of Environmental Science and Health, Part A, 2020
Rushika Patel, Rajesh Chudasama, Rutujaben Solanki, Priya Patel, Krupali Parmar, Nasreen S. Munshi
Automated modeling of the structure by I-Tasser,[30,31] Phyre2.[32] Model evaluation by SAVES server for ERRAT[33] and Verify3D plot,[34,35] Old SWISS-MODEL for PROCHECK[36,37] and ProSA.[38,39] Docking studies with version 1.5.6 of the AutoDockVina. Interactive visualization and analysis of molecular structures and related data, sequence alignments, docking results and conformational ensembles using UCSF Chimera version 1.11.2, Discovery Studio 17.2.0.16349, Pymol 1.3, LigPlus 1.4.5.[40] The supportive hardware used in this study included: Computer: HP AMD A4-5000 APU; Processor: 1.50 GHz; RAM: 4 GB; and Operating system: 64-bit with a × 64-based processor with Windows 8.1.
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.