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PIPER

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

PIPER

Understand and predict protein-protein interactions at the atomic level

PIPER is a well-validated protein-protein docking program based on a multi-staged approach and advanced numerical methods that generates reliable 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.

Key Capabilities

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Easily set up  and run protein-protein docking computations using the intuitive biologics interface, BioLuminate
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Rapidly sample and score billions of relative orientations of interacting proteins using PIPER’s efficient Fast Fourier Transformation (FFT) approach, along with accurate pairwise potentials
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Increase 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 
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Improve results using specialized potentials optimized for specific classes of protein–protein complexes such as antibody-antigen and enzyme-inhibitor pairs
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Use experimental data to bias selection of the correct pose by applying a broad range of constraints, including attractive or repulsive biasing constraints or declare specific residues to be buried
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High-performance free energy calculations for drug discovery

BioLuminate

Comprehensive modeling platform for biologics discovery

Publications

Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

Life Science
Investigating Protein-Peptide Interactions Using the Schr’dinger Computational Suite
Life Science
PIPER: An FFT-based protein docking program with pairwise potentials
Life Science
DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking
Life Science
The 4th meeting on the Critical Assessment of Predicted Interaction (CAPRI) held at the Mare Nostrum, Barcelona
Life Science
Selection of Nanobodies that Block the Enzymatic and Cytotoxic Activities of the Binary Clostridium Difficile Toxin CDT
Life Science
Consensus Induced Fit Docking (cIFD): Methodology, validation, and application to the discovery of novel Crm1 inhibitors

Training & Resources

Online certification courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.

Tutorials

Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.