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Piper Protein-Protein Docking

complex of pollen allergen with antibody

The past decade has seen explosive growth in knowledge of protein-protein interaction networks and how malfunctions in these networks underlie many diseases.  A critical missing link in understanding of these networks, and how particular interactions lead to diseased states, is knowledge of the structure of a protein-protein complex behind an interaction. Protein-protein docking to obtain detailed atomic-level structures of complexes can provide key information for the development of treatments for a wide variety of diseased states.

Accompanying the rise in knowledge of protein-protein interactions, a larger portion of the pharmaceutical industry is now pursuing protein therapeutics as an alternative to traditional small molecules of the past, or in some cases, working to develop antibody-drug conjugates to take advantage of the targeting of antibodies while retaining the cell permeability of existing small molecules.  Through docking to obtain atomic-level detail of an antibody’s CDR interaction with the epitope of an antigen, researchers can obtain critical information to further optimization of affinity for the epitope and allow grafting of the antibody CDR onto a new scaffold for humanization.

Acpharis has an exclusive license to PIPER, a state-of-the-art protein-protein docking program from Boston University.  As the technology behind the ClusPro web server, PIPER has been used by thousands of academic groups worldwide. PIPER combines the well-tested method of using FFT for global sampling of protein-protein interactions with novel algorithms and DARS statistical potentials allowing for excellent scoring in the sampling stage of docking. In the latest evaluation of CAPRI, PIPER was used extensively by the Vajda lab to allow them to be the only group to obtain 6 high or medium quality predictions and was used internally by the ClusPro server to be the only automated server with 5 acceptable predictions (see tables below).  With the team that created PIPER on staff, Acpharis is well-positioned to continue to advance PIPER to meet their customer’s needs.

Acpharis offers services and custom solutions based on PIPER directly to customers. Acpharis has teamed up with Schrodinger to include PIPER as part of their BioLuminate product for sale worldwide.

Acpharis Staff Publications using PIPER

Recent Example Publications using PIPER via the ClusPro Server

Assessment of CAPRI Predictions 2009

Tables S11 and S12 of “Docking and scoring protein interactions: CAPRI 2009” 


  Group Total / High / Medium
1 S. Vajda (Boston University, Boston, MA) 6/4***/2**
2 M. Zacharias (Jacobs University, Bremen, Germany) 6/4***/1**
3 X. Zou (University of Missouri, Columbia, MO) 6/3***/2**
4-5 M. Eisenstein (Weizmann Institute, Rehovot, Israel) 6/3***/1**
H. Wolfson (Tel Aviv University, Tel Aviv, Israel)
6-7 Z. Weng (U. of Massachussets, Worcester, MA) 6/2***/2**
H-X. Zhou (Florida State U., Tallahassee, FL)
8 A. Bonvin (Utrecht University, the Netherlands) 6/1***/4**
9 CLUSPRO (server, Vajda group, Boston University, MA) 5/1***/3**
10 J. Fernandez-Recio (Barcelona Supercomputing C., Spain) 5/2**



1 CLUSPRO (Vajda group, Boston University, Boston MA) 5/1***/3**
2 HADDOCK (Bonvin group, Utrecht University, the Netherlands) 4/1***/1**
3 GRAMM-X (Vakser group, U. of Kansas, Lawrence, KS) 2/2***
4 SKE-DOCK (Takeda-Shitaka group, Kitasato U., Japan) 2/1***
5 PatchDock, FiberDock, FireDock (Wofson group, Tel Aviv U.) 1/1***