Cluspro statistics

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Cluspro specifications


Unique identifier OMICS_03772
Name Cluspro
Alternative names Cluspro 2.0, ClusPro-DC
Interface Web user interface
Restrictions to use None
Input data Two proteins known to interact.
Input format PDB
Output data The displayed models or models for all energy coefficients. All the compiled files can be downloaded in a TAR file which includes four times 30 PDB files.
Output format PDB,TAR
Computer skills Basic
Version 2.0
Stability Stable
Registration required Yes
Maintained Yes


  • person_outline Carlos Camacho <>
  • person_outline Sandor Vajda <>
  • person_outline Dima Kozakov <>

Additional information

Publications for Cluspro

Cluspro in publications

PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854

[…] and their results compared for consistency. specifically, we used the patchdock server () and imposed that the f37 residue in ns5a is located at the binding interface, as described (). we next used cluspro (; ) without any assumption on the residues involved in binding. the best models from cluspro and patchdock were superimposed and revealed an almost identical binding pose. we next checked […]

PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] performed on antibody modeling derived from pigs web server using hyperchem 8.0 professional software[] to further improve the predicted structures., docking was performed using hex 8.0 software, cluspro 2.0 server[] cluspro (, zdock (http://zdock.umassmed. edu/)[], and haddock[] at 2.2/. this scrutiny […]

PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6

[…] these functiones of irak-m in irak1-mediated signaling, docking simulations were performed using a myddosome-based model containing irak1 dd in place of irak2 dd subunits using the program cluspro–. irak-m was docked with a modified myddosome composed of six myd88, four irak4, three irak1 dd subunits, and an empty irak1 dd subunit space. for each of the four scoring schemes applied, […]

PMCID: 5955456
PMID: 29473457
DOI: 10.1080/21505594.2018.1441589

[…] structure was energy minimized similarly to the last step of the initial minimization without any positional constraints., the obtained peptide structure was then docked without restraints with the cluspro 2.0 protein-protein docking tool [, ] to the human igg1 crystal structures that were retrieved from the protein data bank (pdb; both the separate fc domain (pdb id: 4w4n; […]

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

[…] space grid an enormous number of docked receptor-ligand 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 […]

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Cluspro institution(s)
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA; Acpharis Inc., Holliston, MA, USA
Cluspro funding source(s)
Supported by grants R35 GM118078 and R01 GM061867 from the National Institute of General Medical Sciences; and grants DBI 1147082, DBI 1458509; and AF 1527292 from the National Science Foundation.

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