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Protocols

KINARI-Web specifications

Information


Unique identifier OMICS_24593
Name KINARI-Web
Alternative name KINematic And RIgidity Web
Interface Web user interface
Restrictions to use None
Input data A file containing protein structure data.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Ileana Streinu
  • person_outline Ileana Streinu

Additional information


http://kinari.cs.umass.edu/Site/Help/kinariWebQuickStartHelp.html http://kinari.cs.umass.edu/Site/documentation.html#

Publication for KINematic And RIgidity Web

KINARI-Web citations

 (3)
call_split

A conservation and rigidity based method for detecting critical protein residues

2013
BMC Struct Biol
PMCID: 3952096
PMID: 24565061
DOI: 10.1186/1472-6807-13-S1-S6
call_split See protocol

[…] ions of the mechanical model, and hence the protein. In Figure ), we show the cartoon rendering of Staphylococcal Nuclease (PDB ID 1stn). The visualization of its rigidity properties calculated using KINARI-Web are shown in Figure ), where color bodies indicate clusters of atoms that are rigid.In this study, we used KINARI-Mutagen [], which is part of the KINARI [] software, to perform fast evalua […]

library_books

Rigidity analysis of protein biological assemblies and periodic crystal structures

2013
BMC Bioinformatics
PMCID: 3817814
PMID: 24564201
DOI: 10.1186/1471-2105-14-S18-S2

[…] Our computational setup involves the following: we parse the input PDB file, and use the information in it to build the biological unit and desired crystal structure. Then, we apply our KINARI-Web software to place hydrogen atoms, identify chemical interactions, and perform rigidity analysis, which outputs the rigidity clusters. To perform the experiments, we selected a dataset based […]

library_books

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

2013
BMC Bioinformatics
PMCID: 3817810
PMID: 24564209
DOI: 10.1186/1471-2105-14-S18-S3

[…] proof-of-concept, we investigated the use of a single, rigid bar to model these interactions. We have implemented these extensions in our KINARI software, and made it available for public use on the KINARI-Web server []. In addition, we propose a method for evaluating the tuning of the H-bond and hydrophobic energy cutoffs. This is an adaptation of the B-cubed score from the information retrieval […]

Citations

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KINARI-Web institution(s)
Department of Computer Science, University of Massachusetts, Amherst, MA, USA; Department of Computer Science, Ford Hall, Smith College, Northampton, MA, USA
KINARI-Web funding source(s)
Supported by National Science Foundation (DMS-0714934) and the Defense Advanced Research Projects Agency (HR0011- 09-1-0003) grants.

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