About Database

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General information

Database statistics

References

 

General information

The modelling of disulphides has been achieved by using the program called MODIP (MOdelling of DIsulphide bonds in Proteins)(Sowdhamini et al ., 1989) This database contains modelled as well as native disulphide bonds.These disulphide bonds are also graded based on stereochemical quality. For every protein, database provides a list of possible sites to introduce disulphide bonds along with their stereochemical grades.

MODIP

This computer modelling program requires N,C alpha ,C beta coordinates as input and considers all possible residue pairs and calculate the C alpha-C alpha, C beta-C beta distances. It selects the residue pair with C alpha-C alpha distance of less than or equal to 6.5 Angstorm and C beta-C beta distance of less than or equal to 4.5 Angstorm and geometricaly fixes the sulfur atom and grades them based on the stereochemical quality.

Conformational parameters of Disulphide bond

Definition of various dihedral angles in Disulphide bond

Summary of MODIP procedure

Note: For the purpose of generating database relaxation in C alpha-C alpha , and C beta-C beta distances are included

C alpha-C alpha distance - 7 Angstorm

C beta-C beta distance - 4.7 Angstorm

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Database statistics

       
       
 Number of proteins         :   2319
       
 Number of proteins         :    637
   with minimised model
       
 Number of proteins         :   1682
    with multiple model
       
 Number of disulfide bonds  : 747882 
       
 Native disulfide bonds     :  46843
       
 Modelled   "         "     : 701019
       
 Grades                    
       
        A  grade            :  84257
       
        B  grade            : 189010
       
        C  grade              226441
       
        D  grade            : 248174

Option to run MODIP online also available for missing entries

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References

R.Sowdhamini, N.Srinivasan, B.Shoichet, D.V.Santi, C.Ramakrishnan and 
P.Balaram (1989). Stereochemical modelling of disulfide bridges: 
Criteria for introduction into proteins by site-directed mutagenesis.
Prot. Engng., 3, 95-103.

N.Srinivasan, R.Sowdhamini, C.Ramakrishnan and P.Balaram (1990). Conformations 
of disulfide bridges in proteins and peptides. Int. J. Pept. Prot. Res.,
36, 147-155.  

L.E.Donate, E.Gherardi, N.Srinivasan, R.Sowdhamini, S.Aparicio and 
T.L.Blundell (1994). Molecular evolution and domain structure of 
plasminogen-related growth factors (HGF/SF and HGFl/MSP).
Prot. Sci., 3, 2378-2394.

Zhou.H, Mazzulla.M.J, Kaufman.J.D, Stahl.S.J, Wingfield.P.T, Rubin.J.S, 
Bottaro.D.P and Byrd R.A (1998). The solution structure of the N-terminal 
domain of hepatocyte growth factor reveals a potential  heparin-binding site.
Structure., 6(1), 109-16.

D.Y.Chirgadze, J.Hepple, R.A.Byrd, R.Sowdhamini and T.L.Blundell (1998).
Insights into the structure of hepatocyte growth factor scatter factor
(HGF/SF) and implications for receptor activation.
FEBS Letts., 430, 126-129.]





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