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Overview of ZDOCK and RDOCK

Contents


Protein Docking

Among the many recent advances in bioinformatics is the rapid accumulation of 3-dimensional structures of protein complexes through X-ray crystallization. These structures provide many insights on protein-protein interactions, allowing more rational approaches toward drug development and the treatment of disease. However, not all protein complexes have been crystallized, so various computational techniques have been developed to deal with this problem. One of the most promising approaches is protein docking, where the structure of a complex between two proteins is predicted based on the independently crystallized structures of the components.

We have developed two protein docking algorithms, designed to operate in succession: a rigid-body docking program, ZDOCK, and a refinement program, RDOCK. ZDOCK uses a fast Fourier transform to search all possible binding modes for the proteins, evaluating based on shape complementarity, desolvation energy, and electrostatics. The top 2000 predictions from ZDOCK are then given to RDOCK where they are minimized by CHARMM to improve the energies and eliminate clashes, and then the electrostatic and desolvation energies are recomputed by RDOCK (in a more detailed fashion than the calculations performed by ZDOCK). We then tested these programs with a benchmark of 49 non-redundant unbound test cases, where we identified a near-native structure (within 2.5 angstrom from the experimental structure) as the top prediction for 37% of the test cases, and within the top 4 predictions for 49% of the test cases. The superior performance of ZDOCK and RDOCK has also been demonstrated in a community-wide protein docking blind test, CAPRI. Check this out for more details. All software, as well as the benchmark are freely available to academic users. For basic information on running ZDOCK, see this site.


Performance

The performance of our docking software has been demonstrated with the benchmark and the worldwide blind test CAPRI.


References

  • Pierce B, Weng Z (Accepted) M-ZDOCK: A Grid-based Approach for Cn Symmetric Multimer Docking. Bioinformatics.
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  • Mintseris J, Weng Z (2003) Atomic Contact Vectors in Protein-Protein Recognition. Proteins 53: 629-639.
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  • Li L, Chen R (joint first authors), Weng Z (2003) RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins 53: 693-707.
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  • Chen R, Li L, Weng Z (2003) ZDOCK: An Initial-stage Protein-Docking Algorithm. Proteins 52:80-87.
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  • Chen R, Tong W, Mintseris J, Li L, Weng Z (2003) ZDOCK Predictions for the CAPRI Challenge. Proteins 52:68-73.
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  • Chen R, Mintseris J, Janin J, Weng Z (2003) A Protein-Protein Docking Benchmark. Proteins 52:88-91.
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  • Chen R, Weng Z (2003) A Novel Shape Complementarirty Scoring Function for Protein-Protein Docking. Proteins 51:397-408.
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  • Chen R, Weng Z (2002) Docking Unbound Proteins Using Shape Complementarity, Desolvation, and Electrostatics. Proteins 47:281-294.
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Contact Information

ZDOCK Team
Bioinformatics Program
Boston University
44 Cummington Street
Boston, MA 02215
USA
e-mail:ZDOCK team



Protein Engineering