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/content/aca/journal/sdy/3/1/10.1063/1.4942414
2016-02-18
2016-09-30

Abstract

KINematics And RIgidity (KINARI) is an on-going project for flexibility analysis of proteins. The new version of the software,, extends the functionality of our free web server KinariWeb, incorporates advanced web technologies, emphasizes the reproducibility of its experiments, and makes substantially improved tools available to the user. It is designed specifically for , in particular, for (a) very large molecules, including bioassemblies with high degree of symmetry such as viruses and crystals, (b) large collections of related biomolecules, such as those obtained through simulated dilutions, mutations, or conformational changes from various types of dynamics simulations, and (c) is intended to work as seemlessly as possible on the large, idiosyncratic, publicly available repository of biomolecules, the Protein Data Bank. We describe the system design, along with the main data processing, computational, mathematical, and validation challenges underlying this phase of the KINARI project.

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