The sequence-based prediction of beta-residue contacts and beta-sheet structures contain key information for protein structure prediction. However, the determination of beta-sheet structures poses numerous challenges due to long-range beta-residue in...
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have fac...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 9, 2018
Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been p...
A biosensor that could simultaneously detect multi-analyte as many as in a single test is more favored when facing lots of samples for screening purpose. In such a biosensor, the recognition element with broad specificity and highly affinity is a key...
Journal of chemical theory and computation
Oct 9, 2018
The value of protein models obtained with automated protein structure prediction depends primarily on their accuracy. Protein model quality assessment is thus critical to select the model that can best answer biologically relevant questions from an e...
Journal of chemical information and modeling
Sep 7, 2018
Zeolites are important materials for research and industrial applications. Mesopores are often introduced by desilication but other properties are also affected, making its optimization difficult. In this work, we demonstrate that Perturbation Theory...
Food research international (Ottawa, Ont.)
Sep 4, 2018
To elucidate the sequence, origin and structure-activity relationship of antioxidant peptides from sesame protein, sesame protein was hydrolysed by a dual-enzyme system comprised alcalase and trypsin, then this hydrolysate was fractionated by ultrafi...
Journal of chemical information and modeling
Aug 28, 2018
The new wave of successful generative models in machine learning has increased the interest in deep learning driven de novo drug design. However, method comparison is difficult because of various flaws of the currently employed evaluation metrics. We...
Journal of chemical information and modeling
Aug 17, 2018
The most recent version of the Cahn-Ingold-Prelog rules for the determination of stereodescriptors as described in Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013 (the "Blue Book"; Favre and Powell. Royal Society of ...
Estrogen receptor α (ERα) plays a significant role in occurrence of breast cancer and may cause various adverse side-effects when ERα is an off-target protein. A theoretical model was derived to predict the binding affinity of ERα using the pharmacop...