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helps.json
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helps.json
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{
"tool" : "tool_skeleton",
"help" : "method",
"title" : "Method",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\nIn MC-DNA, DNA is represented intrinsically at base pair step level. Rigid base-pairs are connected via elastic potentials modulating the interactions of neighboring base-pairs in a given tetramer environment. The six interactions are given by six base-pair step coordinates: three translational (shift, slide, rise) and three rotational (tilt, roll, twist) degrees of freedom. The parameters of the elastic potentials (stiffness constants and relaxed state) for each base-pair step with its nearest neighbors are derived from atomistic molecular dynamics simulations. \r\n\r\nMC-DNA runs a Metropolis Monte Carlo algorithm on the base-pair step parameters. It then tranforms the bp-step parameters of the final result of the algorithm into a three-dimensional all-atom representation of the DNA molecule.\r\n\r\nImportant note: even though the outputs of this program are atomistic, the smallest unit of this model is a base-pair.\r\n\r\n\r\nOptions: \r\n\r\n* **Create Structure**: Creates a single structure of DNA in a relaxed state (relaxed state is defined as the state of minimum potential energy according to the bp-step parameters)\r\n\r\n* **Create Trajectory**: Creates a certain number of DNA structures (specify the number of structures in the corresponding field). The sampling is done via Monte Carlo moves on the bp-step parameters of the DNA. This option is recommended if average properties of the DNA want to be obtained."
}
{
"tool" : "tool_skeleton",
"help" : "results",
"title" : "Results",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\nIn the ‘View Results’ section, you can download all the analysis results and the structure/trajectory in a compressed tar.gz file.\r\nIn this file you can find the figures of the bending analysis:\r\n\r\nThe results depend on the type of operations the user chooses to execute MC-DNA.\r\n\r\n[Create Structure](#anchor1)\r\n[Create Trajectory](#anchor2)\r\n\r\n\r\n<span id=\"anchor1\"></span>\r\n\r\n \r\n\r\nIf 'Create Structure' chosen:\r\n\r\n* ***create_str01.png***: Bending distribution of all 5/10bp segments of the simulated DNA fiber. The bending angle of a segment of 10 base-pairs of DNA is calculated according to sqrt(b<sub>n</sub><sup>x</sup>(10) <sup>2</sup> + b<sub>n</sub><sup>y</sup>(10) <sup>2</sup>) while b<sub>n</sub><sup>x</sup>(10) and b<sub>n</sub><sup>y</sup>(10) are calculated according to Equation (7) and (8) of Battistini et al., J Mol Bio (2010). The x-axis shows the bending in degree, the y-axis the density.\r\n\r\n![{w:300}](/tools/tool_skeleton/help/img/5a041a4eb2ea41.86588142.png)\r\n\r\n\r\n* ***create_str02.png***: Bending of 5/10bp segments along the DNA fiber. The bending angle of a segment of 10 base-pairs of DNA is calculated according to sqrt(b<sub>n</sub><sup>x</sup>(10) <sup>2</sup> + b<sub>n</sub><sup>y</sup>(10) <sup>2</sup>) while b<sub>n</sub><sup>x</sup>(10) and b<sub>n</sub><sup>y</sup>(10) are calculated according to Equation (7) and (8) of Battistini et al., J Mol Bio (2010) (Note: n here is the last bp of the segment b<sub>n</sub><sup>x</sup>(10) ). The x-axis shows the index of the basepair, the y-axis shows the bending in degree. \r\n\r\n![{w:300}](/tools/tool_skeleton/help/img/5a041bb9575091.47548585.png)\r\n\r\n\r\n<span id=\"anchor2\"></span>\r\n\r\n \r\n\r\nIf 'Create Trajectory' chosen:\r\n\r\n* ***create_traj01.png***: same as create_str01.png, here all snapshots of the trajectory are taken into accoutn.\r\n\r\n![{w:300}](/tools/tool_skeleton/help/img/5a041cbbb2f0b4.02405084.png)\r\n\r\n\r\n\r\n* ***create_traj02.png***: same as create_str02.png, averaged over all snapshots of the trajectory.\r\n\r\n![{w:300}](/tools/tool_skeleton/help/img/5a041cea5aed73.99266157.png)\r\n\r\n\r\nNOTE: For a more detailed analysis apart from bending use the output pdb or trajectory files as an input to *NAflex*."
}
{
"tool" : "tool_skeleton",
"help" : "references",
"title" : "References",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\nMC-DNA"
}
{
"tool" : "tool_skeleton",
"help" : "inputs",
"title" : "Inputs",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\n**MC-DNA** can be computed from a **DNA sequence**.\r\n\r\n# Accepted input file combinations\r\n\r\n**Combination ** *(File Type - Data Type)*\r\n```\r\nTXT DNA sequence\r\n```\r\n\r\nTo run **MC-DNA** a `txt` file representing a **DNA sequence** needs to be selected in the **user workspace**. Associated to the **txt file**, at the right part of the workspace (in the same row), an **Actions button** represented by a **tool** contains all the **MuG VRE** tools that can be called from this particular file. **MC-DNA** is one of the **tools** that can be selected.\r\n\r\n![](/tools/tool_skeleton/help/img/5a04130e8af725.21134042.png)\r\n\r\n\r\nOnce you selected the tool **MC-DNA** you can choose between 'Create Trajectory' and 'Create Structure'.\r\nIf 'Create Trajectory' selected a field 'Number of structures' appears where the user can choose how many snapshots are going to be simulated.\r\n\r\n\r\n![](/tools/tool_skeleton/help/img/5a04131a96cde5.79741321.png)"
}
{
"tool" : "tool_skeleton",
"help" : "outputs",
"title" : "Outputs",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\n![](/tools/tool_skeleton/help/img/5a046ab40f25d1.74493147.png)\r\n\r\nIf 'Create Structure' chosen:\r\n* ***mc_dna_eq_str.pdb***: structure with DNA in relaxed state. Can be visualized in NGL viewer\r\n\r\n![{w:300}](/tools/tool_skeleton/help/img/59fdf8a0359424.68527922.png)\r\n\r\nIf 'Create Trajectory' chosen:\r\n* ***mc_dna_str.dcd***: trajectory file (in GROMACS format). Can be visualized in NGL viewer together with 'mc_dna_str.pdb'\r\n* ***mc_dna_str.pdb***: first structure of the ensemble. Can be visualized it in NGL viewer\r\n* ***mc_dna_str.top***: topology file for DNA trajectory; necessary to visualize trajectory in NGL viewer. It is also necessary for Input to the analysis tool of nuclear acid structures and trajectories *NAflex*\r\n\r\n"
}
{
"tool" : "tool_skeleton",
"help" : "help",
"title" : "Help",
"content" : "<a href=\"/tools/tool_skeleton/help/method.php\" class=\"btn green btn-xs\">Method</a> <a href=\"/tools/tool_skeleton/help/inputs.php\" class=\"btn green btn-xs\">Inputs</a> <a href=\"/tools/tool_skeleton/help/outputs.php\" class=\"btn green btn-xs\">Outputs</a> <a href=\"/tools/tool_skeleton/help/results.php\" class=\"btn green btn-xs\">Results</a> <a href=\"/tools/tool_skeleton/help/references.php\" class=\"btn green btn-xs\">References</a>\r\n\r\n![](/tools/tool_skeleton/help/img/59fdf070e84cd6.10508109.png)\r\n\r\n**MC-DNA** is a tool to rapidly create all-atom B-DNA conformations of a sequence of interest. With this tool the user can obtain ground state structure or a molecular dynamics like trajectory of many posible conformations. With the use of a Monte Carlo algorithm on the bp-step parameters this tool runs up to 10<sup>5</sup> faster than conventional Molecular Dynamics providing similar accuracy. MC-DNA provides a three-dimensional all-atom representation of the DNA structure with the underlying sequence of interest and displays its bending properties.\r\nFurthermore, the obtained structure and/or trajectory can be used as an input to **NAflex** for a more detailed analysis.\r\n\r\n![{w:600}](/tools/tool_skeleton/help/img/5a046f74a7aa28.10745002.png)\r\n\r\n"
}