I am looking for a good tool for examining the effects of mutations in proteins. In particular, one that shows the effects of the mutated residues on adjacent amino acids.
One really good tool for this that I know of is SWISS PDB VIEWER. It will show you the effects of replacing a residue by changing its coordinates, and will show you the changed positions of nearby amino acids (from steric clashes). For example, if I replace a glycine residue with tryptophan, it is inevitable that nearby residues will be effected from steric clashes. This is exactly what I am looking for. Unfortunately, there is no way to automate the process in the program (you have to choose one mutation at a time through a graphic user interface) so it is pointless to use this for a project examining the effects of site directed mutagenesis on many proteins. Even worse, the source code is completely unavailable and the software developers are very strict about others using their software---so splicing the function (which shows the effects of mutated residues on nearby amino acids) out of the program and writing a program myself with it is completely out of the question.
My question would be, given the information posted above on what I am looking for, does anybody know of a good program for this, preferably one with a source code for this? Any kind of help would be vastly appreciated.
One really good tool for this that I know of is SWISS PDB VIEWER. It will show you the effects of replacing a residue by changing its coordinates, and will show you the changed positions of nearby amino acids (from steric clashes). For example, if I replace a glycine residue with tryptophan, it is inevitable that nearby residues will be effected from steric clashes. This is exactly what I am looking for. Unfortunately, there is no way to automate the process in the program (you have to choose one mutation at a time through a graphic user interface) so it is pointless to use this for a project examining the effects of site directed mutagenesis on many proteins. Even worse, the source code is completely unavailable and the software developers are very strict about others using their software---so splicing the function (which shows the effects of mutated residues on nearby amino acids) out of the program and writing a program myself with it is completely out of the question.
My question would be, given the information posted above on what I am looking for, does anybody know of a good program for this, preferably one with a source code for this? Any kind of help would be vastly appreciated.