Databases
User-Created Database
This website allows users to select pairs of PDB files that may reveal a domain movement for input to the DynDom program. If the run is successful then the results are automatically loaded into the database along with all other successful runs. You can browse all the results and make simple searches. It allows us to tap the knowledge of individual specialists around the world to help populate a single database, which can act as a repository of information on protein domain movements.
You can browse and search the protein families. For each family you can find information about its members, clusters and representative conformational pairs, from where you can link to the results of the individual DynDom runs.
Non-Redundant Database
An exhaustive analysis was carried out on all available protein structures in order to build a non-redundant and comprehensive database of protein domain movements. This involved grouping protein conformations into families, clustering the members within each family to remove redundant structures, using a Gram-Schmidt procedure to select representative pairs for each family and finally running the DynDom program to analyse protein domain movements for each family.
You can browse and search the protein families. For each family you can find information about its members, clusters and representative conformational pairs, from where you can link to the results of the individual DynDom runs.
Domain Movement Classification "Hinge and Shear"
1822 domain movements from the Non-Redundant Database have been classified into four groups "No Contact", "Interface-Preserving Movement", "Interface-Creating Movement" and "Mixed".
Interface-Preserving and Interface-Creating have been determined to correspond to "Shear" and "Hinge" movements, respectively, described by Gerstein,
Lesk and Chothia, in their article: "Structural Mechanisms for Domain Movements in Proteins", Biochemistry, Vol33, p6738,1994.
Domain Movement Classification using Dynamic Contact Graphs
1822 domain movements from the Non-Redundant Database have been classified into 16 classes based on an analysis of residue contact changes using Dynamic Contact Graphs.
Ligand-induced domain movements in enzymes
Currently there are 203 domain movements in enzymes with trigger ligands in the database. 150 of them with spaning trigger ligands and 53 of them with non-spanning trigger ligands. For details please see G.Qi, S.Hayward, "Database of ligand-induced domain movements in enzymes",BMC Structural Biology, 9:13, 2009.