CIntX: A Software Tool for Calculating the Intrinsic Exchange Rates of Labile Protons in Proteins

Estimation of extrinsic (kex) and intrinsic (krc) exchange rate constants for labile protons of proteins is indispensable to determine the residuespecific free energies. While kex of labile protons in proteins are determined by experimental methods, the krc of those protons are calculated based on the parameters derived from the model compound studies, in general. We, herein, describe a computational tool, CIntX, which calculates the krc of labile protons in proteins at defined experimental conditions such as pH, temperature, solvents and ionic strength using three-dimensional structures of the proteins. The program also accounts structural parameters (amino acid sequence, cis-trans proline conformations, disulfide bonds and ionisable groups in the proteins) influencing the krc of labile protons in a fully automated manner. The robustness of the tool on predicting the krc of labile protons in proteins has been validated using data reported in the literature. The program is publicly available at http://sblab.sastra.edu/cintx.html