software
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software [2013/10/02 17:13] 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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| + | ---- | ||
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| - | [[vslab|{{:software:volarea:volarea3.jpg?direct&200|}}]] | + | [[vslab|{{:software:vslab:vslab3.png?direct&200|}}]] |
| </WRAP> | </WRAP> | ||
| [[vslab|VsLab - VMD plug-in]] | [[vslab|VsLab - VMD plug-in]] | ||
| + | ### | ||
| vsLab (Virtual Screening LABoratory) is an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques. | vsLab (Virtual Screening LABoratory) is an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques. | ||
| + | ### | ||
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| [[compasm|compASM - VMD plug-in]] | [[compasm|compASM - VMD plug-in]] | ||
| + | ### | ||
| CompASM is an intuitive VMD plug-in for that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. | CompASM is an intuitive VMD plug-in for that allows the user to perform a full Alanine Scanning Mutagenesis (ASM) procedure, requiring only very little user effort. | ||
| + | ### | ||
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| - | [[compasm|{{:software:madamm:madamm1.png?direct&200|}}]] | + | [[madamm|{{:software:madamm:madamm1.png?direct&200|}}]] |
| </WRAP> | </WRAP> | ||
| [[madamm|MADAMM]] | [[madamm|MADAMM]] | ||
| + | ### | ||
| + | MADAMM allows to include a certain degree of flexibility of both the receptor and the ligand during a Multi stAged Docking with an Automated Molecular Modeling protocol. The results obtained with this methodology show that MADAMM can lead to dramatic improvements in both sampling and scoring over conventional single rigid protein docking. | ||
| + | ### | ||
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| + | ---- | ||
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| + | <WRAP column 15%> | ||
| + | [[volarea|{{:software:volarea:volarea3.jpg?direct&200|}}]] | ||
| + | </WRAP> | ||
| + | |||
| + | [[volarea|VolArea]] | ||
| + | ### | ||
| + | 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> | ||
| + | |||
| + | [[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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| + | ---- | ||
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| + | <WRAP column 15%> | ||
| + | [[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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| + | ---- | ||
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| + | <WRAP column 15%> | ||
| + | [[biopathfinder|{{:molup_00003.png?direct&200|}}]] | ||
| + | </WRAP> | ||
| - | MADAMM that to include a certain degree of flexibilization of both the receptor and the ligand during a Multi stAged Docking with an Automated Molecular Modeling protocol. The software uses standard docking software and molecular mechanics force fields in the core process and a set of scripts that automates the process without the intervention of the user. | + | [[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.1380730396.txt.gz · Last modified: 2013/10/02 17:13 by nuno
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