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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


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  • 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 in publications

PMCID: 5955889
PMID: 29650980
DOI: 10.1038/s41598-018-23982-3

[…] conformations, using fast fourier transforms (fft) for energy evaluation. to conduct this initial sampling we use the protein docking server cluspro 2.0 which is based on a docking program called piper. these conformations are then sorted by their energy values, and the top few thousands with the lowest energy are retained for further processing. at the second stage of docking protocols, […]

PMCID: 5446404
PMID: 28550308
DOI: 10.1038/s41467-017-00029-1

[…] .  and supplementary fig.  represent the results of three independent binding experiments., 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 […]

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

[…] 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 […]

PMCID: 4862341
PMID: 27217723
DOI: 10.2147/DDDT.S103393

[…] but also attempts to find the native site under the assumption that it will have a wide free-energy attractor with the largest number of results. it works in three main steps. first, it runs piper, a rigid-body docking program, based on a novel fast fourier transform docking method with pairwise potentials. second, by using a clustering technique for the detection of near-native […]

PMCID: 4780765
PMID: 26950439
DOI: 10.1371/journal.pone.0149097

[…] hbs-ep buffer at 25°c. the spr data analysis was done by applying the biaevaluation v.4.1.1 software (biacore)., protein-protein docking analysis was performed using two fft-based docking software piper [] and zdock []. the in silico experiments were performed using ndpk-b crystal structure (pdb code: 1nue) as the probe and nbd1 crystal structure (pdb code: 1r0x) as the target protein. 1000 […]

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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.