Rosetta 3.1 Release Manual

Fixed Backbone ddG Prediction

This application estimates the impact of a sequence change on a protein's stability. It can perform single mutations as well as multiple mutations. There are a variety of options that can be used to refine the structure (this application is still under developement), but only the fixed backbone monomeric protocol will be introduced and described here. The ddg application is in rosetta_source/src/apps/public/ the name of the application is fix_bb_monomer_ddg.cc

Input Files

the input files are pdb files. Sidechain minimization is recommended for the input structures. The second input file specifies mutations to make. Two formats are currently accepted:

resfiles: option to specify resfile: -resfile The resfile specifies which residues to mutate and what to mutate them into. This will produce single mutations for each of the amino acids specified. Please look at Resfile Syntax for details. If, for example, ALLAA is specified at a certain position, the position will be mutated into the 19 other amino acids and the ddg for each of these 19 mutations will be calculated. EX 1 and EX 2 keywords have no effect on how the structures are refined.

"mutfiles": option to specify mutfile: -ddg:mut_file a file for specifying mutations that supports specification of multiple mutations. The format is as follows: header: the total keyword specifies how many mutations to expect. If the number of mutations listed do not match up with the total number declared, no calculations will be performed. content: each mutation is specified in the following manner: the number of mutations to be made is listed, and on the next line is the wild-type residue, the position of the mutation, and the mutated residue desired. And example of a correctly specified mutfile follows. For this example, we want to specify 3 mutations total. one calculation is a double mutant with an Alanine at position 167 to Phenylalanine and a Thr at position 67 to Ala. The second calculation is a single mutation.

total 3
2
A 167 F
T 67 A
1
I 16 A

Command Lines and Options


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