Kihara Lab Protein Docking Suite

The protein docking suite developed by our group includes programs to perform protein-protein docking prediction, multiple protein docking, as well as protein docking prediction using predicted protein-protein interfaces.

LZerD Protein Docking Server

The LZerD server makes available a graphical web interface for protein-protein docking. Users can easily specify two or more proteins along with any constraints and run docking computations remotely. Users can be notified of results by email or by bookmarking a web link. Algorithms made available through the server include LZerD and Multi-LZerD.

LZerD: Protein-Protein Docking Algorithm

Our pairwise docking program, LZerD (Local 3D Zernike descriptor-based Docking algorithm), uses geometric hashing to generate ligand orientations using the 3D Zernike descriptors as the shape matching criteria. Scoring is based on a shape complementarity term defined by the local shape Zernike and orientation of the surface normals. In addition a clash penalty term and buried surface area have also been incorporated.

Multi-LZerD: Multiple protein docking for asymmetric complexes

Multi-LZerD is a generic multiple protein docking program that can create docking models without additional biological information (like symmetry constraints). It is based on LZerD which uses geometric hashing and the 3D Zernike descriptor for pairwise docking purposes. Based on the pairwise predictions, Multi-LZerD applies a Genetic Algorithm to combine 2-body transformations in order to create a complete protein complex from the original parts. It uses a physics based score to guide the GA towards the best solution possible.

PI-LZerD: Protein Docking Prediction Using Predicted Protein-Protein Interfaces

PI-LZerD uses protein interfaces predictions, from current protein interface prediction methods, in combination with LZerD to iteratively reach higher prediction accuracies.

IDP-LZerD: Intrinsically Disordered Protein Docking

IDP-LZerD uses LZerD to dock intrinsically disordered proteins (IDPs) to structured proteins without prior knowledge of the binding site.

Path-LZerD: Assembly order prediction for multimeric heteroprotein complexes

Path-LZerD, which predicts the assembly order of a protein complex by simulating its assembly process.

Flex-LZerD: Domain-based protein docking with extremely large conformational changes

Flex-LZerD, which docks domains independently to allow a flexible fitting procedure to model the full complex.