Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions.

ABSTRACT:

Summary

Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, w

SUBMITTER: Ribeiro J 

PROVIDER: S-EPMC6748739 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature