Search by MHC Allele:
This search function allows you to access MPID-T by MHC Class, MHC Allele, Organism, Peptide Length and Dataset of your interest . To get the results of all the MHC class I and/or class II structures, choose the MHC Class (i.e. MHC class I, MHC class II or ALL) in the option, select "ALL" in the MHC Allele option, select "ALL" in the Organism option, select "ALL" in the Peptide Length option, and check/uncheck the Non redundant checkbox for the data set you are interested (i.e. redundant or non-redundant).
You can limit the output parameters by customizing the output parameters menu. Select the output parameter of your interest.
Search by PDB Data:
This search function allows you to access MPID-T by PDB ID, Resolution, Release year and Combined querying based on resolution and release year.
To query by PDB ID, enter the valid four letter PDB code (e.g. 1hhj) and click the search button. To enter multiple PDB code, use "," as delimiter as shown in the text area (e.g. 1hhh,1hhj).
To query by Resolution, enter the resolution with two decimals (e.g. 3.20,3.00) and click the search button. To enter multiple resolution, use "," as delimiter (e.g. 3.00,3.20).
To query by PDB release year, enter the release year (e.g. 2001) and click the search button. To enter multiple PDB release year use "," as delimiter (e.g. 2001,2000).
To do a combined query on Resolution and Release year, choose the "AND" option for combined querying and "OR" option to query either by resolution or release year. Click the search button.
Definition of Interaction Parameters:
Total Hydrogen Bonds - Total number of hydrogen bonds between the MHC molecule and its corresponding bound peptide.
Interface Area - The interface area for class I pMHC complexes was define as the change in their solvent accessible surface area when going from a monomeric MHC molecule to a dimeric pMHC complex state. Similarly, the interface area for class II pMHC complexes was defined as the change in their solvent accessible surface area when going from a dimeric MHC molecule to a trimeric pMHC complex state.
Gap Volume - The gap volume gives a measure of the complementarity of the interacting surfaces.
The volume of the gaps between the two interacting subunits is calculated using a program SURFNET (Laskowski, 1991). Each pair of subunit atoms are considered in turn, placing a sphere (maximum radius 5.0 angstroms)
halfway between the surfaces of the two atoms, such that its surface touches the
surfaces of the atoms in the pair. Checks are made to test if any other atoms intercepts
this sphere and each time an intercept is detected the size of the sphere is reduced
accordingly. If at any time the size of the sphere falls below a minimium (minimium radius 1.0 angstroms)
the sphere is discarded. If the sphere remains after all checks, its sizr is recorded. The sizes of all the allowable gap-spheres are then used to calculate
the gap volume between the two subunits.
Gap Index - One essential feature in receptor-ligand binding is the electrostatic
and geometric complementarity observed between associating molecules. Gap index is used as
a means to evaluate the complementarity of interacting surfaces. The gap index
is calculated using the formula Gap Index=Gap Volume/Change in solvent accessible surface area.
Some useful links to MHC-peptide databases are provided below.
MHC-Peptide Interaction Database version 1.2 (MPID)
MHCBN: Comprehensive Database of MHC Binding and Non-Binding Peptides
HLA Informatics Group, ANRI
PAProc (Prediction Algorithm for Proteasomal Cleavages)
(Dr. Kenneth Parker)
Molecular Immunology Database
International Immunogenetics Database
JenPep - Peptide binding database, 8000 entries
HLA Ligand/Motif Database
MHC-Thread: HLA class II predictions
RANKPEP: Prediction of binding peptides to Class I MHC molecules (Dana Farber) (also class II)
ProPred-I: The Promiscuous MHC Class-I Binding Peptide Prediction Server
ProPred: MHC class II binding peptide prediction server
Epitope Prediction (HLA class I + TAP)
PREDICT: Prediction of MHC binding peptides using ANN
Biomolecular Interaction Network Database