software
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software [2013/10/02 17:15] nuno |
software [2017/06/30 11:26] (current) nuno |
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| + | ~~NOTOC~~ | ||
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| + | {{:folder-software.png?direct|}} | ||
| + | </WRAP> | ||
| + | \\ | ||
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| List of Software currently available on the PortoBioComp Database: | List of Software currently available on the PortoBioComp Database: | ||
| + | \\ | ||
| + | ---- | ||
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| - | [[vslab|{{:software:volarea:volarea3.jpg?direct&200|}}]] | + | [[vslab|{{:software:vslab:vslab3.png?direct&200|}}]] |
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| - | [[compasm|{{:software:madamm:madamm1.png?direct&200|}}]] | + | [[madamm|{{:software:madamm:madamm1.png?direct&200|}}]] |
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| ### | ### | ||
| VolArea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. | VolArea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure. | ||
| + | ### | ||
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| + | ---- | ||
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| + | <WRAP column 15%> | ||
| + | [[vmdmagazine|{{:software:vmdmagazine:screenshots:vmdmagazine2.png?direct&200|}}]] | ||
| + | </WRAP> | ||
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| + | [[vmdmagazine|VMDMagazine]] | ||
| + | ### | ||
| + | VMDMagazine was developed with the goal of visualizing scientific information without requiring any prior knowledge of the user in the area of molecular visualization or even molecular modeling. This means that the users (teachers and students) do not have to worry about the handling of molecular visualization software or in the preparation of such types of visualizations that normally involve complex selection steps and the upload of multiple files and scripts. | ||
| + | ### | ||
| + | |||
| + | |||
| + | ---- | ||
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| + | [[biopathfinder|{{:software:biopathfinder:screenshots:biotracker_3.png?direct&200|}}]] | ||
| + | </WRAP> | ||
| + | |||
| + | [[Chem-path-tracker|Chem-path-tracker]] | ||
| + | ### | ||
| + | Chem-path-tracker is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra’s algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. | ||
| + | ### | ||
| + | |||
| + | |||
| + | ---- | ||
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| + | <WRAP column 15%> | ||
| + | [[biopathfinder|{{:molup_00003.png?direct&200|}}]] | ||
| + | </WRAP> | ||
| + | |||
| + | [[molUP|molUP]] | ||
| + | ### | ||
| + | molUP is a VMD extension that provides a simple manner for loading and saving Gaussian files, and analyze related results. molUP provides a graphical interface for VMD where the users can load and save chemical structures in the Gaussian file formats. | ||
| ### | ### | ||
software.1380730553.txt.gz · Last modified: 2013/10/02 17:15 by nuno
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