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Protocols

PIPER specifications

Information


Unique identifier OMICS_18855
Name PIPER
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

Versioning


No version available

Maintainer


  • 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

 (30)
call_split

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

2018
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

call_split

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

2017
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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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Ömer GÜLLÜLÜ

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Desktop
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.