PIPER

A state of the art protein-protein docking program

PIPER: A state of the art protein-protein docking program

PIPER is a state-of-the-art protein-protein docking program based on a multi-staged approach and advanced numerical methods that reliably generates accurate structures of protein-protein complexes. Based on well-validated docking code from the Vajda lab at Boston University, PIPER has a proven track record as an outstanding predictor of protein-protein complexes as judged by previous CAPRI (Critical Assessment of Prediction of Interactions) blind experiments.

The Advantages of Protein-Protein Docking

Protein-protein interactions govern various aspects of structural and functional cellular mechanisms, and their elucidation is crucial for a better understanding of processes such as metabolic control, signal transduction, and gene regulation. While genome-wide proteomics studies provide an increasing list of interacting proteins, only a small fraction of the potential complexes are amenable to direct experimental analysis. Thus, it is important to utilize protein-protein docking methods that can explain the details of specific interactions at the atomic level. Furthermore, the precise understanding of protein-protein interactions for disease-implicated targets is ever more critical for the rational design of biologic-based therapies.

For more information please visit the PIPER website.

Superior accuracy:
PIPER was used to determine the top-scoring entry in the most recent CAPRI blind assessment of protein-protein docking.

Improve results with specialized modes:
PIPER offers specialized modes to improve results, such as docking an antigen to an antibody or docking to form a dimer or a trimer.

Achieve greater levels of control with constraints:
Utilize experimental knowledge to influence the likelihood of specific interactions by applying attractive or repulsive biasing constraints, or declare specific residues to be buried.

Highly efficient protocol:
Unlike other protein-protein docking methods, PIPER’s efficient Fast Fourier Transformation (FFT) approach along with accurate pairwise potentials greatly reduce the number of initial poses that would otherwise require additional rigid-body filters and computationally expensive electrostatic calculations. PIPER also increases the number of near-native conformations in the initial selection of poses relative to other FFT-based docking programs, while reducing the number of false positives such as geometrically distant structures that score well.

Easy-to-use interface:
PIPER is fully integrated with BioLuminate—Schrödinger's easy-to-use biologics interface—allowing protein-protein docking computations to be set up and run before or after other calculations.

Citations and Acknowledgements

Chuang, G-Y.; Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., "DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking," Biophys. J., 2008, 95, 4217-4227

Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., "PIPER: An FFT-based protein docking program with pairwise potentials," Proteins, 2006, 65, 392-406

  1. http://structure.bu.edu/content/protein-protein-docking
  2. http://rosettadesigngroup.com/blog/535/capri-state-of-protein-protein-docking/
  3. http://www.ebi.ac.uk/msd-srv/capri/
  4. Fernández-Recio, J .; Sternberg, M.J.E., “The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona”, Proteins: Structure, Function and Bioinformatics, 2010, 78, 3065-3066. (http://onlinelibrary.wiley.com/doi/10.1002/prot.22801/abstract)

ö "Investigating Protein–Peptide Interactions Using the Schrödinger Computational Suite"

Bhachoo, J.; Beuming, T., Methods Mol Biol., 2017, 1561, 235-254

ö "Selection of Nanobodies that Block the Enzymatic and Cytotoxic Activities of the Binary Clostridium Difficile Toxin CDT"

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ö "Consensus Induced Fit Docking (cIFD): Methodology, validation, and application to the discovery of novel Crm1 inhibitors"

Kalid, O.; Warshaviak, D.T.; Shechter, S.; Sherman, W.; Shacham, S., J. Comput. Aided Mol. Des., 2012, 26, 1217–1228

"The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona"

Fernández-Recio, J.; Sternberg, M.J.E., Proteins, 2010, 78, 3065-3066

"DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking"

Chuang, G-Y.; Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., Biophys. J., 2008, 95, 4217-4227

"PIPER: An FFT-based protein docking program with pairwise potentials"

Kozakov, D.; Brenke, R.; Comeau, S.R.; Vajda, S., Proteins, 2006, 65, 392-406
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