![]() ![]() This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. SASA-based approximations underesti- mated protein–DNA contact surfaces on average by 40%. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visu- alization. Here, we present a versatile software tool and web server for the calculation of contact sur- face areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. 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. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true con- tact surface. 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. Ribeiro, Judemir Ríos-Vera, Carlos Melo, Francisco Schüller, Andreas ![]() ![]() Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions Calculation of accurate interatomic contact surface areas for the quantitative analysis of. ![]()
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