Chemical bonds and interactions between amino
acid side chains determine the two- and three-dimensional fold
and detailed shape of a protein. After modelling the mutated side
chains into the structure, its effect on the chemical bonds with
neighbouring residues and changes in the solvent accessible surface
of the residue atoms can be studied by the following methods.
| CSU |
http://bip.weizmann.ac.il/oca-bin/lpccsu |
Analysis of
interatomic contacts |
(Sobolev, et
al., 1999) |
| KiNG |
http://kinemage.biochem.duke.edu/software/king.php |
Molecular graphics |
(Lovell, et
al., 2003) |
| MolProbity |
http://molprobity.biochem.duke.edu/ |
Analysis of
interatomic contacts and packing, structure validation |
(Davis, et al.,
2004) |
| PROBE |
http://kinemage.biochem.duke.edu/software/probe.php |
Analysis of
interatomic contacts and packing |
(Word, et al.,
2000; Word, et al., 1999) |
| PyMOL |
http://pymol.sourceforge.net/ |
Molecular graphics |
(DeLano, 2002) |
| RankViaContact |
http://bioinf.uta.fi/RankViaContact.html |
Analysis and
visualization of interatomic contacts |
(Shen and Vihinen,
2003) |
| SABLE |
http://sable.cchmc.org/ |
Prediction of
solvent accessibilities, 2D structures and transmembrane
domains |
(Adamczak, et
al., 2004; Adamczak, et al., 2005; Wagner, et al., 2005) |
| CMA |
http://ligin.weizmann.ac.il/cma/ |
|
(Sobolev et al., 2005) |
|
