A different look at the quality of modeled three-dimensional protein structures.

Measuring the accuracy of protein three-dimensional structures is one of the most important problems in protein structure prediction. For structure-based drug design, the accuracy of the binding site is far more important than the accuracy of any other region of the protein. We have developed an automated method for assessing the quality of a protein model by focusing on the set of residues in the small molecule binding site.

Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms.

Motivation: Profile-based protein homology detection algorithms are valuable tools in genome annotation and protein classification. By utilizing information present in the sequences of homologous proteins, profile-based methods are often able to detect extremely weak relationships between protein sequences, as evidenced by the large-scale benchmarking experiments such as CASP and LiveBench.

Results: We study the relationship between the sensitivity of a profile-profile method and the size of the sequence profile, which is defined as the average number of different residue types observed at the profile's positions.