cx programmer dock cross reference window

CX PROGRAMMER DOCK CROSS REFERENCE WINDOW FREE

Information regarding the structure and dynamic behavior of proteins often reveals mechanistic details of their function, which are important in understanding how they carry out their designated tasks. Proteins are large, complex molecules that have many critical roles in cells, thereby determining the structure, characteristics and functions of tissues and organs. The established protocol is expected to take 6-12 days to complete, depending on the size of the proteins and the complexity of the cross-linking data. This protocol is an excellent additional application with which to use cross-linking results for building structural models of proteins.

CX PROGRAMMER DOCK CROSS REFERENCE WINDOW FREE

This modeling protocol is compatible with many cross-linking workflows and uses open-source programs or programs that are free for academic users and do not require expertise in computational modeling. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution.

In the case of protein complexes, the cross-linking data is further used to dock the subunits to one another to generate models of the interacting proteins. The distance restraints are used (i) to adjust preliminary models that are calculated based on a homologous template and primary sequence and (ii) to select the model that is in best agreement with the experimental data.

This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments.

Cx programmer dock cross reference window