PCE: Protein
Continuum Electrostatics
PCE performs the calculation of the
electrostatic potentials for a protein
by solving numerically the Poisson-Boltzmann equation (the Finite
Difference Poisson- Boltzmann method, FDPB). It is a server adaptation
of
the MEAD potential program (MEAD: Macroscopic Electrostatics with
Atomic
Detail, D. Bashford).
Two types
of services are currently proposed: electrostatic potentials
calculation and pKa
calculations.
Access the services:
More information:
PCE potentials
calculated with MEAD
Input:
- You can upload a pdb
file :
A PDB formatted file. You may
edit the file to remove all information
not
necessary for the computations.
- or give an ID
You can specify the code of the PDB entry. It must be on the form: 1tim
,
or 1timA. The latter specification will restrict the computation to
chain A
of the 1tim PDB entry.
- Alternatively, the users can upload
a
PQR file with different forcefield parameters.
When using a PDB file
as input, the current
version
assumes that GLU, ASP, C-term are charged negatively and ARG, LYS,
N-term
are charged positively. Partial charges (PARSE parameters; Sitkoff et
al.
1994 J Phys Chem 98, 1978-88) are assigned on all atoms.
Warnings:
-
Starting from a PDB file as input, this
service currently takes into account only protein atoms but work is in
progress to consider hetero-atoms.
- A pdb file could include a number of
protein structures (like many NMR structures), thus be sure you select
the
appropriate structure, with regard to NMR file, at present, only the
first
structure will be considered.
Calculation
parameters:
- Protein
internal dielectric:
The dielectric value inside the protein. Reasonable values are between
1
and 10. The default value is 4.
- Solvent
dielectric:
The dielectric value of the solvent. A value of 80 (the default value)
is
frequently used.
- Ionic
strength:
A value for the ionic strength. If unsure, use 0.1 M.
- Optional
specifications:
- You can write a set of coordinate points inside or outside the
protein
into
a file and obtain the potentials at these points. The expected format
of the data is series of three dimensional x y z coordinates, one
coordinate per line, numbers only, no comma as separator (e.g. 2.34
5.36 8.34).
- Color ranges:
You can select the range for color coding the protein surface.
- Images:
You can select the format, image size... If the output is in gif
format,
you will obtain an animated (rotation around the Y axis) image of your
protein.
Results:
- Electrostatic
potentials are displayed on the molecular
surface
with a color-code (red negative, blue positive) with DINO. Optionally,
the service will return the potential values at coordinates specified
by the user.
PCE
pKa
calculations with MEAD
PCE performs calculations of the pKa values of
titratable groups in
proteins.This approach implies calculation of the intrinsic pKa values
of
all titratable groups (defined as the pKa of one titratable group if
all
other titratable groups in the protein were held in their neutral
forms),
as well as the pair-wise electrostatic interactions between the
titratable
groups.
PARSE parameters are used in the present version of PCE.
Input:
- You can upload
a pdb file :
A PDB formatted file. You may
edit the file to remove all information
not
necessary for the computations.
- or give an ID
You can specify the code of the PDB entry. It must be on the form:
1tim,
or 1timA. The latter specification will restrict the computation to
chain A
of the 1tim PDB entry.
Warning: A pdb file could
include a number of
protein structures (like many NMR structures), thus be sure you select
the
appropriate structure, with regard to NMR file, at present, only the
first
structure will be considered.
Calculation
parameters:
- Protein
internal dielectric:
The dielectric value inside the protein. Reasonable values are between
2
and 20. The default value is 4.
- Solvent
dielectric:
The dielectric value of the solvent. A value of 80 (the default value)
is
frequently used.
- Ionic
strength:
A value for the ionic strength. If unsure, use 0.1 M.
- Specification
of
the titratable sites:
At present, users can specify if Tyr and Cys are titratable or not.
Output file:
- PCE will return pKint, pK1/2, pH-dependent protonation curves of
all
titratable groups, estimated pI and Electrostatic interaction energy
(kcal/mole) between titratable groups.