Smoking tobacco and physical inactivity are key preventable behavioural risk factors of cardiovascular disease (CVD). Computerised coaching systems can help individuals to modify risky behaviours, thereby preventing CVD. However, most reported eHealth or computerized coaching systems are hard to reuse in slightly different settings. To provide an open-source, reusable computer coaching system, we developed Perfect Fit. The reusability is manifested by building around the open-source text- and voice-based contextual assistant framework Rasa. Rasa provides a simple, standard interface to many popular messaging and voice channels, and custom connectors are easily implemented. A set of algorithms have been developed and connected to Rasa to drive and personalize the conversation flow and the coaching process. Such algorithms make use of data stored in a devoted database. Furthermore, Perfect Fit adheres to best practices and standards in software engineering. The modular design of Perfect Fit will allow researchers to connect the virtual coach to any messaging or voice channel with only modest modification. Perfect Fit is available under open-source license in GitHub and is currently in prototype-phase. Concluding, Perfect Fit will deliver a virtual coach that can easily be adapted and reused in different settings. The coach helps individuals to achieve and maintain abstinence from smoking and sufficient physical activity (PA).

MOTIVATION: Protein complexes play critical roles in many aspects of biological functions. Three-dimensional (3D) structures of protein complexes are critical for gaining insights into structural bases of interactions and their roles in the biomolecular pathways that orchestrate key cellular processes. Because of the expense and effort associated with experimental determinations of 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D structures of biomolecular complexes. Despite recent progress, reliably distinguishing near-native docking conformations from a large number of candidate conformations, the so-called scoring problem, remains a major challenge. RESULTS: Here we present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms with a score obtained using a graph representation of the protein-protein interfaces and a measure of evolutionary conservation. It achieves a scoring performance competitive with, or superior to, that of state-of-the-art scoring functions on two independent datasets: (i) Docking software-specific models and (ii) the CAPRI score set generated by a wide variety of docking approaches (i.e. docking software-non-specific). iScore ranks among the top scoring approaches on the CAPRI score set (13 targets) when compared with the 37 scoring groups in CAPRI. The results demonstrate the utility of combining evolutionary, topological and energetic information for scoring docked conformations. This work represents the first successful demonstration of graph kernels to protein interfaces for effective discrimination of near-native and non-native conformations of protein complexes. AVAILABILITY AND IMPLEMENTATION: The iScore code is freely available from Github: https://github.com/DeepRank/iScore (DOI: 10.5281/zenodo.2630567). And the docking models used are available from SBGrid: https://data.sbgrid.org/dataset/684). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a combination of simple structural properties, such as the residue-contacts made at the interface, PRODIGY has demonstrated a top performance compared with other state-of-the-art predictors in the literature. Here we present an extension of it, named PRODIGY-LIG, aimed at the prediction of affinity in protein-small ligand complexes. The predictive method, properly readapted for small ligand by making use of atomic instead of residue contacts, has been successfully applied for the blind prediction of 102 protein-ligand complexes during the D3R Grand Challenge 2. PRODIGY-LIG has the advantage of being simple, generic and applicable to any kind of protein-ligand complex. It provides an automatic, fast and user-friendly tool ensuring broad accessibility. AVAILABILITY AND IMPLEMENTATION: PRODIGY-LIG is freely available without registration requirements at http://milou.science.uu.nl/services/PRODIGY-LIG.