Abstract: The methods of the invention relate to improved methods for determining the optimal sequence alignments between a first protein sequence and a second protein sequence based upon the information from multiple reference structure-structure alignments.

Abstract: The present invention relates to improved methods for determining functional residues on the surface of a query protein. The claimed methods rely on determining a plurality of functional annotation scores for a query protein and comparing these functional annotation scores to distributions of similar functional annotation scores derived from a plurality of reference proteins. Based upon these comparisons, a putative functional cluster may be annotated as a functional cluster or a non-functional cluster.

Abstract: The present invention relates to methods and systems for sorting a plurality of protein structures generated by a database search based upon their corresponding sequences. The methods and systems according to the invention are based upon computer generated graphical user interfaces that present to the user: i) a multiple sequence alignment of the sequences corresponding to the structures to be sorted; ii) the means to identify whether one or more of the sequences comprise homologous alignment domains; and iii) the means to select one or more sequences for subsequent processing of their corresponding structures. In another aspect of the invention, the user is presented one or more phylogenetic tree representations of user selected homologous alignment domains so that the user may quickly determine the evolutionary similarity of a family of homologous alignment domains.

Abstract: A preferred embodiment of the invention is a method for determining a preferred sequence alignment between a query sequence and one or more template sequences comprising the steps of: 1) aligning at least two reference sequences to determine one or more BRIDGE/BULGE gaps; 2) determining an alignment score between each potential alignment of the query sequence and each template sequence based on whether or not a given sequence alignment between the query sequence and each template sequence creates a BRIDGE/BULGE gap and 3) determining a preferred sequence alignment based on the alignment scores of the query sequence with each template sequence.