POPS

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Provided by:
Fraternali Group @ King's College London     Thomas Young Centre
Jens Kleinjung @ The Francis Crick Institute

Server Version 1.0.6; POPS* Version 1.8.0


INPUT OPTIONS
  Enter a PDB identifier:
  OR Upload a PDB file:

MODE OPTIONS
  coarse-grained calculation
  probe radius

OUTPUT OPTIONS
  molecule composition
  atom types
  molecule topology
  POPS* area per chain
  POPS* area per residue
  POPS* area per atom
  neighbour list

Help on Options


Overview

POPS* is a fast algorithm to calculate solvent accessible surface areas (SASAs) of proteins and nucleic acids at atomic (default) and residue (coarse-grained) level. Atomic and residue area parameters have been optimised versus an accurate all-atom method (Naccess). Residue areas (coarse-grained) are simulated with a single sphere centered at the C-alpha atom for amino acids and at the P atom for nucleotides.

An analytical formula is used for the calculation of solvent accessibilities. The formula is simple, easily derivable and fast to compute, therefore, practical for use in molecular dynamics (MD) simulations as an approximation to the first solvation shell. The default output contains: list of hydrophobic, hydrophilic and total contributions to the accessible surface area of the entire molecule (all atoms), first model only.

After submission a holding page provides access to the result page. Otherwise results (also of previous runs) can be accessed through the Retrieve function.

The POPS* program code can be downloaded here.
Users publishing results obtained with the POPS* program should acknowledge its use by citing Fraternali and Cavallo (2002) and for the POPS* server Cavallo et al. (2003).


Parameters

The optimised parameters are listed here:


Help on Options

PDB structure file
Entering a PDB identifier (lower case or upper case without the extension .pdb) in the first text window will automatically perform the POPS* calculation on the corresponding structure. Uploading of structure files by the user can be performed by specifying the file path and name in the second text window. Please ensure that atom and residue names conform to the PDB format.
coarse-grained
Calculation of accessible surface area on residue level.
probe radius
The radius of the surface probe (solvent molecule) in Angstrom.
multiple models (option currently disabled)
By default the POPS* calculation will be performed on the first model only, if a structure file containing multiple models is chosen/uploaded. Activation of the 'Multiple models' button triggers POPS* calculation of all models.
molecule composition
Number of chains, standard residues, total residues and atoms.
atom types
List of atom types and their POPS* parameters.
molecule topology
Number of bonds, angles, torsions and non-bonded interactions.
POPS* area per atom
List of atom areas [A2], number of overlaps and atom grouping (1: positive, 2: negative, 3: polar, 4: aromatic, 5: aliphatic).
POPS* area per residue
List of residue areas [A2] (hydrophilic, hydrophobic, total) and number of overlaps.
POPS* area per chain
List of chain areas [A2] (hydrophilic, hydrophobic, total).
neighbour list
List of neighbours per atom, provided in a separate output file.

Output

ATOM SASAs
AtomNr : atom number in molecular coordinate file
AtomNe : atom name in molecular coordinate file
ResidNe : residue name in molecular coordinate file
Chain : chain name in molecular coordinate file (can be void)
ResidNr : residue number in molecular coordinate file
SASA/A^2 : solvent accessible surace area in Angstrom^2 units
Q(SASA) : quotient of SASA and Surf (below), i.e. the fraction of SASA
N(overl) : number of overlaps with atom neighbours
AtomTp : atom type code (GROMOS van der Waals atom type)
AtomGp : atom group code: positive=1, negative=2, polar=3, aromatic=4, aliphatic=5
Surf/A^2 : surface area of isolated atom

RESIDUE SASAs
ResidNe : residue name in molecular coordinate file
Chain : chain name in molecular coordinate file (can be void)
ResidNr : residue number in molecular coordinate file
Phob/A^2 : hydrophobic solvent accessible surace area in Angstrom^2 units
Phil/A^2 : hydrophilic solvent accessible surace area in Angstrom^2 units
Total/A^2 : total solvent accessible surace area in Angstrom^2 units
Q(SASA) : quotient of SASA and Surf (below), i.e. the fraction of SASA
N(overl) : number of overlaps with atom neighbours
Surf/A^2 : surface area of isolated atom

CHAIN SASAs
Chain : chain number
Id : chain name in molecular coordinate file (can be void)
AtomRange : range of atom numbers in chain
ResidRange : range of residue numbers in chain
Phob/A^2 : hydrophobic solvent accessible surace area in Angstrom^2 units
Phil/A^2 : hydrophilic solvent accessible surace area in Angstrom^2 units
Total/A^2 : total solvent accessible surace area in Angstrom^2 units

MOLECULE SASAs
Phob/A^2 : hydrophobic solvent accessible surace area in Angstrom^2 units
Phil/A^2 : hydrophilic solvent accessible surace area in Angstrom^2 units
Total/A^2 : total solvent accessible surace area in Angstrom^2 units

Background Information

The area equation is defined by a product Π of terms that estimate the reduction of SASA of atom i by the overlap with its neighbours j (Hasel at al., 1988):

Πi=1N [ 1 - (pi pij bij(rij) / Si) ].

i is the atom for which the POPS* area is computed, j is any of N neighbour atoms.
pi is an atom type specific SASA parameter.
pij is a sphere overlap parameter depending on the degree of bonding between i and j (1-2, 1-3, 1-4, 1-(>4)).
bij is a geometric construct based on the radii and distance (rij) of i and j.
Si is the SASA of the free atom i (no neighbours).

The atom specific parameters (radii, SASAs) are listed in the Parameters files for the atoms of all standard PDB residues, followed by the connectivity parameters (pij, bij) and the solvent radius for water.


References

  1. Fraternali, F. and van Gunsteren, W.F.
    An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
    Journal of Molecular Biology 256 (1996) 939-948.   [PubMed Abstract]
  2. Fraternali, F. and Cavallo, L.
    Parameter optimized surfaces (POPS*): analysis of key interactions and conformational changes in the ribosome.
    Nucleic Acids Research 30 (2002) 2950-2960.   [PDF]
  3. Cavallo, L., Kleinjung, J. and Fraternali, F.
    POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level.
    Nucleic Acids Research 31 (2003) 3364-3366.   [PDF]
  4. Kleinjung, J. and Fraternali, F.
    POPSCOMP: an automated interaction analysis of biomolecular complexes.
    Nucleic Acids Research 33 (2005) W342-W346.   [PDF]


The POPS server was developed by Franca Fraternali, the POPS logo was designed by Domenico Fraternali.   Contact Authors

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