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.

  1. 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).
  2. 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:

pkabenchmark


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