A common problem in the conversion of molecular data file formats is the annotation of amino acid and nucleic acid residues not explicitly represented in �small molecule� file formats describing only element type and 3D co-ordinates or atomic connectivity. This problem has limited the interoperability between chemical information processing programs and has led to the situation where molecular graphics programs currently treat the same molecule differently depending upon the file format that it is stored in. An algorithm has been developed to rapidly identify polypeptides and nucleic acids from simple connectivity that can assign standard atom names, residue names, residue numbers and chain identifiers to each atom, and bond orders to each bond.  One of the features of this algorithm is a very efficient method for identifying a sidechain from a set of rooted graphs, which has running time linear in the number of atoms in the sidechain.

Efficient perception of proteins and nucleic acids from atomic connectivity

243rd National Meeting (2012)

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