( E) The four communities (red, gray, purple and green) that contain both protein and RNA nodes.
( D) Edges (green) bridging the interface between GluRS and the tRNA. ( C) Optimal and suboptimal paths (green) between Glu-AMP in the active site and U35 in the tRNA anticodon. Edge thickness is greater between more highly correlated nodes. ( B) Network (green) weighted by correlated motion from MD simulations. Various network visualizations for GluRS tRNA Glu Glu-AMP.
As networks are increasingly used to study the function and dynamics of biological macromolecules, the informative display of network data directly onto 3D representations of biomolecules is needed ( Bhattacharyya and Vishveshwara, 2011 Csermely et al., 2010 Daily et al., 2008 Süel et al., 2002). Residues essential for molecular recognition and reaction mechanisms at different states of the system can be determined by using molecular dynamics (MD) simulations to calculate variations in contacts and displaying the resulting interaction networks and their properties directly onto the 3D structure ( Alexander et al., 2010).
Networkview 36 pdf#
The Interaction Network image can be saved in an SVG or PDF formats by clicking on the “Save image as” button on the top right of the PTM Interaction Network Visualization window.The usefulness of 2D contact network visualization in the study of protein function has already been demonstrated ( Rahat et al., 2009 Sethi et al., 2009) leading to the development of software to display these networks ( Doncheva et al., 2011). Alternatively you can click the magnifying glass icons on the top right of the PTM Interaction Network Visualisation window. If there is a specific PTM you are interested in, you can click on it to zoom onto it and the kinases it has been associated with. See figure legend for additional details. The colour of the circles corresponds to the number of mutations occurring in the kinase with white being none, and dark blue being a normalized maximum. These PTMs originate from your protein of interest (circle with a dark border) which links it to a kinase (circle with thick border). Each PTM is visualized as a different colour box listing the mutation location and the surrounding amino acid sequence. The PTM Interaction Network provides visualization of all PTMs which mediate an interaction between your protein of interest and protein kinases. To select specific ethnic background(s), de-select “All ethnicities” prior to making your selection(s). Population (1000 Genomes): Similar to ESP 6500, this genome sequencing dataset allows you to select mutations reported in specific ethnic backgrounds. Population (ESP6500): this dataset allows you to selected mutations reported in either European American or African American individuals based on exome sequencing of thousands of individuals. To select a specific clinical significance and/or disease, de-select that “All clinical significance” and/or “All disease names” prior to making you selection(s). Selection this option will provide you with two submenus: “Clinical significance” and “Disease name”. To select specific cancer type(s), de-select “All cancer types”, and then select the cancer type(s) you are interested in – multiple selection can be made.Ĭlinical (ClinVar): this dataset allows you to select mutations based on their clinical and pathological significance, and disease in which that clinical significance was detected in based on data on the ClinVar database. This option allows you to select the source of mutation data, which in turn also allows you to select different mutation subsets in the respective submenu (appears once you select the dataset source).Ĭancer (TCGA PanCancerAtlas): this exome sequencing dataset allows you to select mutations based on the cancer type in which the mutation was detected.
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