KINARI-Web: A Server for Protein Rigidity Analysis

Naomi Fox, University of Massachusetts Amherst
Filip Jagodzinski, University of Massachusetts Amherst
Yang Li, Smith College
Ileana Streinu, University of Massachusetts Amherst

Archived as published.

Abstract

KINARI-Web is an interactive web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, adding hydrogen atoms and identifying stabilizing interactions. KINARI-Web offers a quick-start option for beginners, and highly customizable features for the experienced user. Chains, residues or atoms, as well as stabilizing constraints can be selected, removed or added, and the user can designate how different chemical interactions should be modeled during rigidity analysis. The enhanced Jmol-based visualizer allows for zooming in, highlighting or investigating different calculated rigidity properties of a molecular structure. KINARI-Web is freely available at http://kinari.cs.umass.edu. © 2011 The Author(s).