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PIPER specifications


Unique identifier OMICS_18855
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Free trial Yes
Maintained Yes


No version available


  • person_outline Sandor Vajda

Additional information

https://structure.bu.edu/content/protein-protein-docking A registration is needed to access to tools.

Publication for PIPER

PIPER citations


Protein docking refinement by convex underestimation in the low dimensional subspace of encounter complexes

Sci Rep
PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3
call_split See protocol

[…] ffect of the density based clustering component built into SSDU where fitting multiple underestimators seems inevitable. Input preparation consists of two steps: (1) running global FFT sampling using PIPER; and (2) filtering the conformations to retain the top 1000 and 1500 for enzymes/antibodies and other types, respectively. These top energy conformations are supplied as the input to the SSDU al […]


In silico analysis of protein toxin and bacteriocins from Lactobacillus paracasei SD1 genome and available online databases

PLoS One
PMCID: 5570283
PMID: 28837656
DOI: 10.1371/journal.pone.0183548

[…] from S. mutans strain ATCC 700610/UA159 (SMTL id: 3tto.1.A, X-RAY DIFFRACTION 3.30 Å, residue 159–1058) with 48.95% sequence identity, respectively Then, protein-protein docking was performed by the PIPER program [] on the ClusPro 2.0 server [–]. The model with the largest cluster and the lowest docking score of the balance mode was selected. Afterwards, the selected model was elucidated by the P […]


Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria Specific Insert in the Class III RNR Homolog

Front Microbiol
PMCID: 5535262
PMID: 28824557
DOI: 10.3389/fmicb.2017.01409

[…] s to yield refined atomic contacts of protein–protein complexes. Its scoring function takes into consideration both geometric fit and atomic desolvation energy (). On the other hand, ClusPro utilizes PIPER, a rigid body docking program, which is based on a novel Fast-Fourier Transform (FTT) docking approach with pairwise potential. Its scoring function is thus based on pairwise interaction potenti […]


Fortilin binds IRE1α and prevents ER stress from signaling apoptotic cell death

Nat Commun
PMCID: 5446404
PMID: 28550308
DOI: 10.1038/s41467-017-00029-1
call_split See protocol

[…] To study how fortilin and IRE1α interact with each other, we performed a molecular docking experiment using Piper software on the ClusPro Server 2.0 and the crystal structures of fortilin (2HR9) and IRE1α (4U6R) available from the Protein Data Bank. We evaluated docking results using clustering analysis and […]


The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design

PMCID: 5374430
PMID: 28230762
DOI: 10.3390/ph10010026

[…] was retrieved through a genetic algorithm based molecular docking (Gold software, genetic algorithm), while the CK2-peptide substrate complex was obtained through a protein-protein docking procedure (PIPER software []). 1000 complexes were obtained from protein-protein docking algorithms and clusterized using the pairwise Root Mean Square Deviation (RMSD) into the six largest clusters. The final c […]


Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales

PLoS One
PMCID: 5315409
PMID: 28212383
DOI: 10.1371/journal.pone.0172176

[…] m which is aimed to yield the good molecular shape complementarity of protein-protein complexes []. Its scoring function includes both geometric fit and atomic desolvation energy []. ClusPro utilizes PIPER, a rigid body docking program [], which is based on a novel FFT based docking approach with pairwise potential [,]. The structures with maximum cluster size and the conformation closest to the s […]

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PIPER institution(s)
Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA
PIPER funding source(s)
Partially supported by SolMap Pharmaceuticals, Inc., in collaboration with Mercury Computer Systems and grant GM61867 from the National Institute of Health.

PIPER review

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Performs effective docking process. Also you can pre-process (fill missed atoms and loops, energy minimization etc.) before docking. I think that this program gives the best final docking models of your interested proteins compared to their real interactions.