Contact Prediction is Hardest for the Most Informative Contacts, but Improves with the Incorporation of Contact Potentials

Co-evolution between pairs of residues in a multiple sequence alignment (MSA) of homologous proteins has long been proposed as an indicator of structural contacts. Recently, several methods, such as direct-coupling analysis (DCA) and MetaPSICOV, have been shown to achieve impressive rates of contact prediction by taking advantage of considerable sequence data. In this paper, we show that prediction success rates are highly sensitive to the structural definition of a contact, with more permissive definitions (i.e., those classifying more pairs as true contacts) naturally leading to higher positive predictive rates, but at the expense of the amount of structural information contributed by each contact. Thus, the remaining limitations of contact prediction algorithms are most noticeable in conjunction with geometrically restrictive contacts—precisely those that contribute more information in structure prediction. We suggest that to improve prediction rates for such “informative” contacts one could combine co-evolution scores with additional indicators of contact likelihood. Specifically, we find that when a pair of co-varying positions in an MSA is occupied by residue pairs with favorable statistical contact energies, that pair is more likely to represent a true contact. We show that combining a contact potential metric with DCA or MetaPSICOV performs considerably better than DCA or MetaPSICOV alone, respectively. This is true regardless of contact definition, but especially true for stricter and more informative contact definitions. In summary, this work outlines some remaining challenges to be addressed in contact prediction and proposes and validates a promising direction towards improvement

3D biofabrication for tubular tissue engineering

The therapeutic replacement of diseased tubular tissue is hindered by the availability and suitability of current donor, autologous and synthetically derived protheses. Artificially created, tissue engineered, constructs have the potential to alleviate these concerns with reduced auto-immune response, high anatomical accuracy, long term patency and growth potential. The advent of 3D bio-printing technology has further supplemented the technological toolbox, opening up new biofabrication research opportunities and expanding the therapeutic potential of the field. In this review, we highlight the challenges facing those seeking to create artificial tubular tissue with its associated complex macro and microscopic architecture. Current biofabrication approaches, including 3D printing techniques, are reviewed and future directions suggested

The Strayed Reveller, No. 2

The second issue of The Strayed Reveller.https://scholarworks.sfasu.edu/reveller/1001/thumbnail.jp