Standalone Software

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<tr><td>&nbsp;&nbsp; <font color='#04B4AE' size='5'>Name of Software</td></font><td> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color='#04B4AE' size='5'>Description</td><td>&nbsp;&nbsp; <font color='#04B4AE' size='5'>Category</td></font><td></tr>
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| <font size="5" color="#04B4AE">Name of Software</font>
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<tr><td><a href="http://bip.weizmann.ac.il/oca-bin/lpccsu" target=new>LPC</a></td><td>Analysis of interatomic Contacts in Ligand-Protein complexes.</td><td>Analysis Ligand-Protein interaction</td></tr>
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| <font size="5" color="#04B4AE">Description</font>
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| <font size="5" color="#04B4AE">Category</font>
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<tr><td><a href="http://bip.weizmann.ac.il/oca-bin/lpccsu" target=new>CSU</a></td><td>Analysis of interatomic contacts in protein entries.</td><td>Analysis of interatomic contacts in protein.</td></tr>
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<tr><td><a href="http://www.msi.umn.edu/software/promotif/" target=new>PROMOTIF</a></td><td>PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files.</td><td>Analyses protein structural motifs</td></tr>
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<tr><td><a href="http://fpocket.sourceforge.net/" target=new>fpocket</a></td><td>fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. </td><td>Protein pocket (cavity) detection</td></tr>
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<tr><td><a href="http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/" target=new>Procheck</a></td><td>PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.</td><td>Stereochemical analysis</td></tr>
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[http://bip.weizmann.ac.il/oca-bin/lpccsu LPC]
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<tr><td><a href="http://swift.cmbi.kun.nl/gv/dssp/" target=new>DSSP</a></td><td>The DSSP is software to standardize secondary structure assignment.</td><td>Protein secondary structure</td></tr>
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| Analysis of interatomic Contacts in Ligand-Protein complexes.
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| Analysis Ligand-Protein interaction
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<tr><td><a href="http://globin.bio.warwick.ac.uk/psipred" target=new>Psipred</a></td><td>Psipred is a protein structure prediction software.</td><td>Protein secondary structure</td></tr>
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<tr><td><a href="http://www.bioinf.manchester.ac.uk/naccess/" target=new>Naccess</a></td><td>Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids.</td><td>Solvent Accessible Area Calculations</td></tr>
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[http://bip.weizmann.ac.il/oca-bin/lpccsu CSU]
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</table>
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| Analysis of interatomic contacts in protein entries.
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| Analysis of interatomic contacts in protein.
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|-
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|
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[http://www.msi.umn.edu/software/promotif/ PROMOTIF]
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| PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files.
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| Analyses protein structural motifs
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|-
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|
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[http://fpocket.sourceforge.net/ fpocket]
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| fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation.
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| Protein pocket (cavity) detection
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|-
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|
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[http://www.ebi.ac.uk/thornton-srv/software/PROCHECK/ Procheck]
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| PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
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| Stereochemical analysis
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|-
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|
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[http://swift.cmbi.kun.nl/gv/dssp/ DSSP]
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| The DSSP is software to standardize secondary structure assignment.
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| Protein secondary structure
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|-
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|
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[http://globin.bio.warwick.ac.uk/psipred Psipred]
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| Psipred is a protein structure prediction software.
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| Protein secondary structure
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|-
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|
 +
[http://www.bioinf.manchester.ac.uk/naccess/ Naccess]
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| Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids.
 +
| Solvent Accessible Area Calculations
 +
|}

Revision as of 18:52, 24 October 2011

Name of Software Description Category

LPC

Analysis of interatomic Contacts in Ligand-Protein complexes. Analysis Ligand-Protein interaction

CSU

Analysis of interatomic contacts in protein entries. Analysis of interatomic contacts in protein.

PROMOTIF

PROMOTIF provides details of the location and types of structural motifs in proteins of known structure by analysis of Brookhaven format coordinate files. Analyses protein structural motifs

fpocket

fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. Protein pocket (cavity) detection

Procheck

PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. Stereochemical analysis

DSSP

The DSSP is software to standardize secondary structure assignment. Protein secondary structure

Psipred

Psipred is a protein structure prediction software. Protein secondary structure

Naccess

Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids. Solvent Accessible Area Calculations
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