About DSDBASE
General information
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 procedureNote: 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 Database statistics
Disulphide Bond Details in DSDBASE
Database
Non-redundant
PDB (April-2001)
No. of Proteins
1,131
13,513
Native
950
22,588
Modelled
46,568
1,491,597
A grade
6,191
195,564
B grade
12,474
400,305
C grade
28,853
462,406
D grade
- *
455,910
Total
47,518
1,514,185* In Non-redundant dataset both C and D grades are merged as C grades.
Option to run MODIP online also available for missing entries
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.]