Supplementary material for the paper: Characterization of Local Geometry of Protein Surfaces with the Visibility Criteria

Bin Li1, Srinivasan Turuvekere2, Manish Agrawal2, Karthik Ramani2Daisuke Kihara3,1,4,5
1 Department of Computer Science, College of Science
3 Department of Biological Sciences, College of Science
2 Department of Mechanical Engineering, College of Engineering
4 Markey Center for Structural Biology
5 The Bindley Bioscience Center

Purdue University, West Lafayette, IN, 47907, USA

1. 48 proteins: 
==> 48set.dat listed 48 bounded, unbounded protein, and RMSD values
Bound    Unbound  RMSD (A)
1a6w.pdb 1a6u.pdb 0.34
1mrg.pdb 1ahc.pdb 0.43
1rne.pdb 1bbs.pdb 0.61
1rbp.pdb 1brq.pdb 0.62
1byb.pdb 1bya.pdb 0.43
1hfc.pdb 1cge.pdb 0.37
3gch.pdb 1chg.pdb 1.10
1blh.pdb 1djb.pdb 0.23
1inc.pdb 1esa.pdb 0.21
...

==> index48.txt listed 48 boundes, unbounded protein with corresponding chains, also with the ligand name, some proteins have more than one ligand, totally there are 65 ligands. 
Bounded Chain UnBounded Chain Ligand
1bid - 3tms - CBX
1bid - 3tms - UMP
1cdo A 8adh - NAD
1dwd - 1hxf - MID
1fbp A 2fbp A AMP
1fbp A 2fbp A F6P
1gca - 1gcg - GAL
1hew - 1hel - NAG
1hyt - 1npc - DMS
...

2. 86 proteins 
==> 86set.datlisted 86 bounded, unbounded protein, and RMSD values
Bound    Unbound  RMSD (A)
1ad4.pdb 1ad1.pdb 0.50
1ahx.pdb 1ahg.pdb 0.24
1aur.pdb 1auo.pdb 0.20
1axz.pdb 1axy.pdb 0.12
1gn8.pdb 1b6t.pdb 0.51
1b9z.pdb 1b90.pdb 0.54
1lri.pdb 1beo.pdb 1.05
1bul.pdb 1bue.pdb 0.18
1byd.pdb 1bya.pdb 0.43
...

==> index86.txt listed 86 boundes, unbounded protein with corresponding chains, also with the ligand name.
Bounded Chain UnBounded Chain Ligand
1a80 - 1hw6 A NAP
1ad4 A 1ad1 A PTP
1ahx A 1ahg A HCI
1aur A 1auo A PMS
1axz - 1axy - GLA
1b9z A 1b90 A MAL
1bht A 1nk1 A EPE
1bk9 - 1psj - PBP
1bul - 1bue A AP3
...

3. Example of input parameters of NAMD
NAMD need the namd file, for example: 182l.X.BZF.namd , to run the simulation, in namd file, the pdb file 182l.X.BZF.pdb, the psf file, 182l.X.BZF.psf and par_all22_prot.inp are needed to run the simulation. usually run: namd2 182l.X.BZF.namd will do the simulation. The ligand file is 182l.BZF. Zipped all files are in 182l.tar.gz.

4. Tar files of distorted structures
The 960 distorted structures are zipped in distorted.tar.gz. (48M)

Contact Information:

Lilly Bld. B235
Department of Biological Sciences
Purdue University
West Lafayette , IN, 47906
Tel: 765-494-2744
Email: dkihara@purdue.edu
lib@purdue.edu