|Multiple Alignment of Protein Binding Sites
Recognizes Spatial Chemical Binding Patterns Common to a Set of Protein Structures
The 5 top ranking solutions are presented. Each solution can be
viewed with Jmol by clicking on the "View solution with Jmol". In
addition the PDB file with the superimposition of all the complexes
can be downloaded as a separated file (aligned.pdb).
The details of the following column fields can be found below (click to jump to a description):
The protein chain, followed by the identity of the amino acid
The one letter amino acid code. However it must be noted that the method is based on the physico-chemical properties and does not consider the identity of the amino acids. These are only displayed for the convenience of analysis.
The physico-chemical property that is matched by the algorithm. The method is based on a representation of each amino acid of a protein as a set of features that are important for its interaction with other molecules. The abbreviations of these features are:
DON - Hydrogen bond donor
ACC - Hydrogen bond acceptor
DAC - Hydrogen bond donor and acceptor (e.g in histidine)
ALI - Aliphatic Hydrophobic property
PII - Aromatic property (pi contacts)
This field specifies whether the matched property is contributed by the backbone or the side-chain of the amino acid.
The abbreviations are:
b - feature contributed by the backbone
s - feature contributed by the backbone
The distance in space measured between the matched features.
Marks the features shared by the two molecules that are contributed by residues with the same identity of the amino acid.
Stage 5 - Jmol options:
Each solution can be visualized with Jmol. The default view presents the superimposition of all the complexes, with their corresponding ligands and the matched physico-chemical properties. The molecules are colored by model (according to the order of input molecules, the first is cyan, the second is magenta, the third is yellow). The physico-chemical properties (pseudocenters) are represented as balls. Hydrogen bond donors are blue, acceptors - red, donors/acceptors - green, hydrophobic aliphatic - orange and aromatic - gray. The surface points that have a similar location in all the molecules are represented as smaller dots with the same coloring.
The "Radio groups" at the bottom allow to hide the protein molecules and focus on the physico-chemical properties, the ligands or the amino acids.
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Reference: Shatsky M, Shulman-Peleg A, Nussinov R, Wolfson H.J. The Multiple Common Point Set Problem and its Application to Molecule Binding Pattern Detection, J. Comp. Biol., 2006, Vol 13, pp. 407-428.