Solvation Free Energy Analysis (SFE)

Mihaly Varadi - 4th Jul 2017

EXECUTIVE SUMMARY

This report details the analysis of the ensemble data stored in the PED regarding the ** solvation free energy** of the conformers (stored in PDB format).

1 Data assembly

The following PED entries were considered for the analysis:

PED1AAB, PED1AAD, PED2AAA, PED2AAD, PED3AAA, PED3AAD, PED4AAB, PED5AAA, PED5AAB, PED5AAD, PED6AAC, PED7AAC, PED9AAC

A random subset of 1000 folded proteins was retrieved from the Protein Data Bank. The criteria were: unique, single chain, protein structures with maximum 30% similarity. Therefore the reference set of folded proteins contained:

• 1,000 PDB files
• and 232,890 residues

The PDB files are saved in the REF subdirectory.

2 Explorative analysis

2.1 PED dataset

2.2 PED dataset

2.3 PED dataset

2.4 Folded reference dataset