Saturday, 15 November 2014
Software: Predicting Solvent Accessibility of Amino Acid residues in proteins
These softwares can be used to obtain info regarding solvent accessibility of amino acid residues in proteins, among other things (such as structure for DSSP).
Get Area links to the web server.
Get Area: http://curie.utmb.edu/getarea.html
DSSP: http://swift.cmbi.ru.nl/gv/dssp/
Surface Racer: http://pharmacy.mc.uky.edu/faculty/tsodikov/software.php
MolMol: http://sourceforge.net/projects/molmol/
Jmol: http://jmol.sourceforge.net/
1. Get Area: quickly calculate solvent accessible surface area or solvation energy
2. DSSP: Provides solvent accessibility and protein structural info.
3. Surface Racer: calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside
4. MolMol: molecular analysis and display program. Can also output accessible surface area.
5. Jmol: Computing a solvent accessible surface area using Jmol. Link (below) to a non-affiliated blog showing you how to get solvent accessible surface area by running a script in Jmol. http://molecularmodelingbasics.blogspot.ca/2014/11/computing-accessible-surface-area-using.html
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