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Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein ... Figure 1. MERMAID web server interface.

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Presentation on theme: "Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein ... Figure 1. MERMAID web server interface."— Presentation transcript:

1 Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein ... Figure 1. MERMAID web server interface (Start page, Parameter page): MERMAID provides two ways to submit a protein structure: a) from OPM database, or b) the user can upload the protein structure from a local system. After uploading the protein structure, MERMAID will redirect the user to parameter page. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz416, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 2. Workflow of the web server
Figure 2. Workflow of the web server. The submitted protein structure is then converted into coarse-grained structure ... Figure 2. Workflow of the web server. The submitted protein structure is then converted into coarse-grained structure and inserted into CG membrane to form a complex structure. The structure then undergoes minimization, equilibration and production run respectively. Every phase of the coarse-grained simulation is analysed and can be visualised. Lastly, all the results can be downloaded from our server. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz416, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 3. MERMAID server output
Figure 3. MERMAID server output. The upper panel shows the trimeric protein structure of the E. coli OmpF porin (PDB ... Figure 3. MERMAID server output. The upper panel shows the trimeric protein structure of the E. coli OmpF porin (PDB accession code: 3POX) in (A) atomistic description, (B) initial coarse-grained structure embedded in a coarse-grained membrane, (C) coarse-grained structure from the last frame of production run. A list of the analysis performed on the CG simulation (D). (E–H) shows the plots for temperature, pressure, system density, and system volume respectively. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact Nucleic Acids Res, gkz416, The content of this slide may be subject to copyright: please see the slide notes for details.

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