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21	21	The structures of the AC isoforms were created via homology modelling using the same template. The region where there are significant structural differences between the isoforms is in a flexible loop region that was not defined in the template structure. There are also variations in sequence length across AC isoforms in this region.
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	23	+[[Tong et al. (2016)>>https://doi.org/10.1002/prot.25167]]
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24		-.. |doi_tong| raw:: html
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27		- <a href="https:~/~/doi.org/10.1002/prot.25167" target="_blank">Tong et al (2016)</a>
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30	30	== Procedure ==
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34	34	~* Structure of AC5 is visualized. The catalytic domain of AC5 is a dimer consisting of two protein chains. In the full structure of AC5 these two chains are connected by a series of transmembrane helices that anchor the protein in the post-synaptic membrane.
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	29	+~* Then the ##PDB2PQR## method is used to generate hydrogen atoms in the protein structure. Proteins contain a number of ionisable amino acids, which can exist in different protonation states, depending on the pH of the solution they are in. ##PDB2PQR## can predict the states of these amino acids, at a given pH (defined as 7.4 in the last cell, a normal physiological pH), then add all missing hydrogen atoms to the structure, and assign atomic charges and radii to all atoms. By default, ##multipipsa## assigns charges and radii from the Amber force field.
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37		-~* Then the Pdb2Pqr method is used to generate hydrogen atoms in the protein structure. Proteins contain a number of ionisable amino acids, which can exist in different protonation states, depending on the pH of the solution they are in. PDB2PQR can predict the states of these amino acids, at a given pH (defined as 7.4 in the last cell, a normal physiological pH), then add all missing hydrogen atoms to the structure, and assign atomic charges and radii to all atoms. By default, multipipsa assigns charges and radii from the Amber force field.
	31	+~* The  ##APBS## method used to solve the linearised Poisson-Boltzmann equation to obtain the electrostatic potential in the dx and ##UHBD## file formats. It also creates a dx file describing the solvent excluded volume of AC5. This is used for visualisation later.
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40		-~* The  APBS method used to solve the linearised Poisson-Boltzmann equation to obtain the electrostatic potential in the dx and UHBD file formats. It also creates a dx file describing the solvent excluded volume of AC5. This is used for visualisation later.
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43	43	~* Finally, electrostatic similarity between AC isoforms is computed.
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45	45	== Results ==
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47		-The similarity of AC5 isoforms is indicated by the surface color from the most dissimilar regions (:math:`SI_{12}=-1`, shown in red) to the highly similar regions (:math:`SI_{12}=1`, shown in white):
	37	+The similarity of AC5 isoforms is indicated by the surface color from the most dissimilar regions ({{formula}}SI_{12}=-1{{/formula}}, shown in red) to the highly similar regions ({{formula}}SI_{12}=1{{/formula}}, shown in white):
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	39	+(% style="text-align:center" %)
	40	+[[image:Similarity.png||alt="Electrostatic Similarity" height="349" width="500"]]
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50		-.. figure:: Similarity.png
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