Selection protocol for soluble proteins
We compiled the 3D-strcuture of soluble proteins from PDB_SELECT entry, as following procedure
- Using the recent PDB_SELECT entries based on 25% sequence identity cutoff. (Number of chains: 901)
- Excluded from all entries are the membrane proteins. (Number of chains: 901 -> 889)
- Excluded from 889 entries are the NMR structures. (Number of chains: 889 -> 742)
- Check on unsuitable entries with lacking of atom coordinates or having of non-sequenctial residues, from 742 chains. (Number of chains: 742 -> 663)
- Assingment of secondary structure regions by PDB discription.
- Compiling the proteins, having helices longer than 19 amino acid residues or potential long helices (bending type). (Total number of chains: 663 -> 397)