KINARI is a suite of tools for calculating and analyzing the rigidity and flexibility of biomolecules. It currently is composed of two applications, KINARI-Web and KINARI-Mutagen. To access either of these two application, click on the "Access" button below.

See related publications, case studies, and profiling information. Check the requirements for supported browsers and platforms. Submit questions and comments with the feedback form.

If you use KINARI-Web for research that you publish, please cite: Naomi Fox, Filip Jagodzinski, Yang Li, Ileana Streinu.
KINARI-Web: A Server for Protein Rigidity Analysis, Nucleic Acids Research, 39 (Web Server Issue), 2011.

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.

Quick-Start performs a streamlined curation and analysis using default options. 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.

Quick-Start

Provide a protein 4-characterPDB Code
(eg 1hvr)
Advanced Users

Select chains, add/remove ligands, designate modeling options, etc.

Download a PDB file, select chains & ligands, add hydrogen atoms, identify interactions
Description

curation results 1HVR

KINARI-Curation is a suite of tools to clean a PDB file. A protein structure file is downloaded from the Protein Data Bank, or a custom PDB-formatted file is uploaded.

Desired chain and ligands are retained, and water molecules can be excluded. The figure on the left shows Chain A only and the ligand of PDB file 1HVR (HIV-1 Protease). Chemical bonds are identified.

Curation Quick-Start invokes default options, while Advanced Users may retain desired parts of a protein, modify or add constraints, or prune constraints according to an energy threshold.

Quick-Start Curation

Provide a protein 4-character PDB Code
(eg 1hhp)
Advanced Users

Add/remove Ligands, H2O, chains, etc.

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.