KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules, developed in Ileana Streinu's research group, LinkageLab. To access the KINARI-Web or KINARI-Mutagen tool, select that application's tab and click on the "Access" button. If you use KINARI for research that you publish, please cite:

 Curate a PDB file, analyze its rigidity, and Visualize the Results
Description

Rigidity Results lysozyme 2LZM

KINARI-Web performs rigidity analysis of a protein, and provides a Jmol-based visualizer to explore the results. The protein can be curated prior to the analysis using our tools. The rigid regions of lysozyme from Bacteriophage T4 are shown on the right.

The curation, rigidity analysis, and visualizer tools in KINARI can also be used as stand-alone applications via the tabs above. Video tutorials and help/documentation are available for each application.

A Quick-Start option performs a streamlined curation and analysis using default paramters. For Advanced Users, the whole functionality of each individual application is available to retain desired chains or ligands, add or remove stabilizing constraints, add hydrogen atoms, and set modeling options.

 Generate in-silico mutants of a protein from a PDB file, and analyze their rigidity.
Description

KINARI-Mutagen 1HHP

KINARI-Mutagen performs in silico mutation experiments on protein structures from the Protein Data Bank, and analyzes their rigidity. A Jmol-scripted embedded visualizer displays the rigidity results for each mutant, and several plots are generated to help the user determine which mutation affected most the protein's rigidity. Residues whose mutation affects the rigidity of the protein can be inferred to be critical.

To generate a mutation at a user-specified residue, KINARI-Mutagen removes hydrogen bonds and hydrophobic interactions from the protein's molecular model. We call this an excision, and it is structurally equivalent to substituting a residue to a glycine.

Calculate the Rigid Regions of a Protein
Description

KINARI molecular modeling

KINARI-Rigidity models proteins as a body-bar-hinge framework. An efficient combinatorial pebble game algorithm is used to analyze the associated graph of the molecular model, to infer flexibile regions of the biomolecule.

The body-bar-hinge framework is based on a concept of rigid bodies, with varying degrees of freedom between them. If pair-wise distances between atoms are determined by the existing covalent bond length and angle constraints, then the atoms are placed into a single rigid body. Along the protein's backbone (shown right, top), peptide units are modeled as rigid bodies (right, bottom). The Advanced Users options are used to designate how each chemical constraint should be modeled.

Advanced Users

Use the advanced feature to specify how chemical constraints should be modeled.

Explore the Rigid Regions of a Protein using a Jmol-based Visualizer
Description

KINARI molecular visualizer

Use the KINARI-Visualizer tool to zoom in on, select, highlight, or hide from view different rigidity properties of a protein. Hydrogen bonds and hydrophobic interactions can be displayed, along with detected hinge axes and rigid clusters.

A hydrogen bond (green) as well as a hinge among two bodies, are shown in the image on the near-right. Two rigid clusters (colored pink and purple) are selected and shown in the image on the far-right, while the other parts of the protein are displayed in gray.

Advanced Users

Select largest bodies, view and highlight hinge regions, display constraints, etc.

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