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Protocols

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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Documentation


Publication for kClust

kClust citations

 (37)
library_books

Repertoire Analysis of Antibody CDR H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification

2018
Front Immunol
PMCID: 5840193
PMID: 29545810
DOI: 10.3389/fimmu.2018.00413

[…] Similar 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 s […]

library_books

Docking, thermodynamics and molecular dynamics (MD) studies of a non canonical protease inhibitor, MP 4, from Mucuna pruriens

2018
Sci Rep
PMCID: 5766534
PMID: 29330385
DOI: 10.1038/s41598-017-18733-9

[…] ER trajectories at an interval of 1 ns. The extracted frames were clustered for comparative analyses of conformational ensembles obtained from 15 °C and 25 °C simulations. Clustering was performed by kclust utility in the MMTSB (Multiscale Modeling Tools for Structural Biology) suite with clustering radius of 2.0 Å from the centroid for backbone, Cα. Various types of structural properties were eva […]

library_books

A computational approach for designing D proteins with non canonical amino acid optimised binding affinity

2017
PLoS One
PMCID: 5673230
PMID: 29108013
DOI: 10.1371/journal.pone.0187524

[…] ut 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 s […]

library_books

A New Generation of Arachidonic Acid Analogues as Potential Neurological Agent Targeting Cytosolic Phospholipase A2

2017
Sci Rep
PMCID: 5651845
PMID: 29057981
DOI: 10.1038/s41598-017-13996-8

[…] hods). 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 identified […]

library_books

Effect of Protonation State and N Acetylation of Chitosan on Its Interaction with Xanthan Gum: A Molecular Dynamics Simulation Study

2017
Mar Drugs
PMCID: 5666406
PMID: 28946687
DOI: 10.3390/md15100298

[…] the PTRAJ module of the AMBER 11 tools []. Visualization of the outputs and MD calculations were undertaken using VMD 1.8.6 software []. In order to obtain physically meaning average structures, the kclust tool was used from the MMTSB package []. A large cut-off was set to include all snapshots extracted from the corresponding trajectories in one cluster, and the structure that was nearest to the […]

library_books

A Molecular Modeling Study of the Hydroxyflutamide Resistance Mechanism Induced by Androgen Receptor Mutations

2017
Int J Mol Sci
PMCID: 5618476
PMID: 28832499
DOI: 10.3390/ijms18091823

[…] s and the last 10 ns stable trajectories were used to calculate the hydrogen bond. The MMTSB toolset was employed to calculate the most populated conformations through a cluster analysis based on the kclust algorithm []. Then, from the largest cluster, the conformation with the lowest RMSD to the cluster center was selected. […]


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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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