Benchmark set (epsilon=8)
Purpose
In order to do pKa calculations on a big pool of representative protein structures, this small set of protein structures with known residua pKas is calculated and benchmarked. Here are information I am looking for from this set of benchmark caculations.
Proper pKa offset numbers in parameter file "extra.tpl". MCCE calculations put system errors and unknown pKa shifting factors as an offset value in this file. If the offset value is 0, then all the factors are just those included in MCCE (desolvation energy, pairwise interaction, backbone and torsion energy etc).
How different the pKa could be from different structures of the same protein. This is measured by the standard deviation of pKas of the same residue, calculated by different structures.
Structures
B1 domain of protein G
1pga.a
2qmt.a
2gi9.a
3gb1.a
B2 domain of protein G
1igd.a
2igd.a
1igc.a
Barnase
1a2p.a
1bnj.a
1bni.a
BPTI
1bhc.a
4pti.a
1bpi.a
6pti.a
RNaseA
3rn3.a
9rat.a
1kf3.a
2e3w.a
Calbindin D9k
3icb.a
1ig5.a
4icb.a
1igv.a
Cardiotoxin A5
1kxi.a
1kxi.b
1cvo.a
CD2d1
1cdc.a
1cdc.b
Chymotrypsin inhibitor 2
2ci2.i
1coa.i
2sni.i
Cryptogein
1beo.a
1beg.a
Epidermal growth factor
1egf.a
3egf.a
1epg.a
1eph.a
Lysozyme (hen)
4lzt.a
1lse.a
2vb1.a
1iee.a
Ribinuclease H1
1rdd.a
2rn2.a
1rch.a
Xylanase
1xnb.a
1bvv.a
2b42.b
3hd8.b
Parameters
portal2net:E08 jmao$ cat extra.tpl
#EXTRA energy: correction of system error on self energy to
# match calc. and exp.
EXTRA ARG+1 0.0
EXTRA ASP-1 -0.85
EXTRA GLU-1 -0.3
EXTRA CTR-1 0.0
EXTRA HIS+1 -1.00
EXTRA LYS+1 0.40
EXTRA NTG+1 -1.3
EXTRA NTR+1 -1.3
EXTRA PAA-1 1.0
EXTRA PDD-1 1.0
EXTRA TYR-1 -0.5
SCALING VDW0 0.125
SCALING VDW1 0.125
SCALING VDW 0.125
SCALING TORS 0.125
Results
The above is calculated against experimental pKa. The number of residues are listed below:
Residue total deviation
ASP- 61 0.05
CTR- 7 0.01
GLU- 56 -0.05
HIS+ 11 0.06
LYS+ 23 0.05
NTR+ 2 0.05
TYR- 7 -0.03
The full list is available here: