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kClust specifications

Information


Unique identifier OMICS_05154
Name kClust
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for kClust

kClust in publications

 (28)
PMCID: 5840193
PMID: 29545810
DOI: 10.3389/fimmu.2018.00413

[…] to a previous work (), a total of 2,000 evenly spaced frames from each trajectory were clustered based on rmsd of the cα and cβ atoms using the k-means clustering algorithm implemented in the kclust module in the mmtsb tool set (). the cluster radius was adjusted to maintain 20 clusters in each trajectory. the structure closest to the center of each cluster was chosen as a representative […]

PMCID: 5766534
PMID: 29330385
DOI: 10.1038/s41598-017-18733-9

[…] of mp-4-trypsin complex at 15 °c was stable at an rmsd of 3.0å–4.0 å and at 25 °c at 3.5å-4.5 å (fig. ). frames from both runs were clustered with a radius of 2 å of cα from the centroid using kclust utility of mmtsb toolkit in amber14. the number of clusters indicates inherent flexibility in the molecule to adopt different conformational states permissive for optimal binding. nine […]

PMCID: 5673230
PMID: 29108013
DOI: 10.1371/journal.pone.0187524

[…] for both temperature and pressure regulation[]. during calculations a snapshot was saved every 2 ps. clustering of the of the 50 ns production trajectory was carried out using the mmtsb toolset[] (kclust tool) to produce a manageably sized, representative ensemble for design calculations. radius was set to 2.0 å and maxerr to 1. this generated a set of 14 backbones representative of the space […]

PMCID: 5651845
PMID: 29057981
DOI: 10.1038/s41598-017-13996-8

[…] the complete model of cpla2 remained stable during the simulation. the conformations sampled during the last 50 ns of the md simulations were clustered into conformational sub-states using the kclust program from the mmtsb tool set, with an rmsd of 2 å set as cutoff. the cluster centroids of the top 5 most populated clusters were used for docking calculations., docking calculations […]

PMCID: 5618476
PMID: 28832499
DOI: 10.3390/ijms18091823

[…] was performed to find the representative structures from the md trajectory for the six systems to explore the different binding modes and interaction mechanisms between hf and wt/mutant ars. kclust algorithm was used for the cluster analysis with a cutoff value of 1.2 å. the systems of hf/wt ar, hf/w741c ar, hf/f876l ar, hf/t877a ar, hf/f876l_t877a, and hf/w741c_t877a ar were clustered […]


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kClust institution(s)
Gene Center and Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany

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