Cluspro statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Cluspro
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Tool usage distribution map

This map represents all the scientific publications referring to Cluspro per scientific context
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Associated diseases

This word cloud represents Cluspro usage per disease context
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Popular tool citations

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Protocols

Cluspro specifications

Information


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

Maintainers


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

Additional information


https://cluspro.bu.edu/help.php

Publications for Cluspro

Cluspro citations

 (227)
call_split

Evolutionary Analysis Provides Insight Into the Origin and Adaptation of HCV

2018
Front Microbiol
PMCID: 5938362
PMID: 29765366
DOI: 10.3389/fmicb.2018.00854
call_split See protocol

[…] d 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 tha […]

library_books

Ofatumumab Monoclonal Antibody Affinity Maturation Through in silico Modeling

2018
PMCID: 5889503
DOI: 10.22034/ibj.22.3.180

[…] Docking was performed using Hex 8.0 software, ClusPro 2.0 server[] cluspro (https://cluspro.bu.edu/publications.php), ZDOCK (http://zdock.umassmed. edu/)[], and HADDOCK[] at http://haddock.science.uu.nl/services/HADDOCK 2.2/. This scrutiny was us […]

library_books

A molecular dynamics study of adenylyl cyclase: The impact of ATP and G protein binding

2018
PLoS One
PMCID: 5918993
PMID: 29694437
DOI: 10.1371/journal.pone.0196207

[…] for the simulations. The starting conformations for the AC5+Gsα and the AC5+ATP+Gsα complexes were obtained by molecular docking starting from the homology models of isolated AC5 and of Gsα using the Cluspro webserver []. The resulting positions of Gsα were close to those observed in the 1AZS and 1CJK complexes (0.8–1.5 Å for the binding α-helix of Gsα and 2.3–2.6 Å for the full backbone), althoug […]

library_books

The IL 33 PIN1 IRAK M axis is critical for type 2 immunity in IL 33 induced allergic airway inflammation

2018
Nat Commun
PMCID: 5913134
PMID: 29686383
DOI: 10.1038/s41467-018-03886-6

[…] Docking simulations were performed using the protein docking prediction server ClusPro (https://cluspro.bu.edu/home.php). ClusPro can simulate protein docking of oligomer forms, which was essential for the studies performed here,. The mutated IRAK-M residues (R56D and Y61E) were […]

library_books

An ecoimmunological approach to study evolutionary and ancient links between coagulation, complement and Innate immunity

2018
PMCID: 5955456
PMID: 29473457
DOI: 10.1080/21505594.2018.1441589

[…] ame 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; www.rcsb.org/pdb). Both the separate Fc domain (PDB ID: 4W4N; re […]

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

[…] ape complementarity, making them relatively easier cases. In fact, considering a wide spectrum of docking test cases in terms of difficulty, enables us to examine the performance gain compared to the ClusPro server in different scenarios. Moreover, other types of complexes present an opportunity to evaluate the effect of the density based clustering component built into SSDU where fitting multiple […]


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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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