title: KINARI-Web: a server for protein rigidity analysis.
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.
authors.affiliation: Department of Computer Science, 140 Governors Drive, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Naomi
authors.initials: N
authors.lastname: Fox
authors.forename: Filip
authors.initials: F
authors.lastname: Jagodzinski
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.forename: Ileana
authors.initials: I
authors.lastname: Streinu
mesh_terms: D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D012984:Software
chemical_list: D008024:Ligands