We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were

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Organisms are constantly bombarded with DNA damaging factors from sources both within and outside their cells. In response, complex repair pathways have evolved to handle all types of DNA damage, such as double and single strand breaks and base oxidation. Different pathways invoke a variety of signaling and repair enzymes, and accurate measurement of the recruitment timescales and interplay between repair protein kinetics is paramount to mapping these damage responses. One popular method to this end is laser microirradiation. While t1/2 and exponential fitting methods have been used historically to quantify microirradiation data, they typically lack the ability to compare values with those obtained from other biophysical methods, such as FRAP, and neglect the effect of nuclear shape on recruitment dynamics. To this end, we present qFADD.py, an open source implementation of our previously developed Q-FADD algorithm, to fit diffusion-based recruitment models that directly account for nuclear shape and size to experimental data. Using replicate simulations in a grid-search algorithm, qFADD.py provides statistically robust estimates with minimal user bias and overhead. Poly(ADP-ribose) polymerase 1 is presented as an example use case.

Metal ions play important biological roles e.g.: activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly.In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e. calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.

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