Scoring Function to Predict Solubility Mutagenesis

Paper (pdf)

List of all mutations (ordered the same way as Table 1 in the paper) - SolMut_Dataset.xls
Input files (with all 137 mutants) for use with the program: input_mutpdbs.txt    input_listmuts.txt

Confusion matrices for all predictions.

Cross validation across sequentially diverse folds, and average hydrophobicity calculations: SeqkfoldCV_AvgHydrophobicity.xls

Script files to draw triangles in VMD for 1VQB.pdb and 2ACY.pdb: 1vqb_9A_triangles.txt    2acy_9A_triangles.txt
    (Load the PDB file into VMD, and then play the corresponding script file.)

• Linux (compiled using gcc version 4.3.0 20080428 on Red Hat 4.3.0-8): OptWtSolMutate.exe
• Mac (Mac OS X, version 10.5.6): Mac_OptWtSolMutate.exe
• The following files should be present in the same directory as the executable for the program to run:
  • Table_Buried_3BPots.txt - 1540 x 27 table of 3-body log-likelihood values
  • ListOfOptWts.txt - list of optimal weights (w_i) to be used with the scoring function (from the LP running on the entire dataset of mutants) .
        Each line has the index of a triplet type, and the value. The index varies from 1 to 41580 (=1540 x 27), while the value lies between 0 and 2.
        The weights of triplets not mentioned in this file are taken as 1 (default value).
  • Readme_OptWtSolMutate.txt - instructions for running the programs.
  • Files mentioned in Readme: list_solmut.txt and input_mutate.txt
  • ResidueMap.txt - maps of residues used in the scoring function.