Local polarity analysis: a sensitive method that discriminates between native proteins and incorrectly folded models

摘要: The evaluation of calculated protein structures is an important step in the design cycle. Known criteria for this assessment proteins are polar and apolar, accessible buried surface area, electrostatic interactions other between atoms (e.g. H..O, S..S), atomic packing, analysis amino acid environment charge distribution. We show that a powerful test accuracy structure can be derived by analysing water contact additionally taking into account their polarity. On basis estimated reference values fraction typical globular with known (mean, SD distribution), misfolded improved significantly. moving windows different length (3-99 residues) over sequence. Model proteins, which included Brookhaven databank, deliberately hypothetical predicted diagnosed as at least partially incorrectly folded. local fault, mostly observed, groups too frequently interior protein. database-derived quantities useful screening designed prior to experimentation may also errors experimentally determined structures.