MOTIVATION: Studies have shown that the accuracy of random forest (RF)-based scoring functions (SFs), such as RF-Score-v3, increases with more training samples, whereas that of classical SFs, such as X-Score, does not. Nevertheless, the impact of the similarity between training and test samples on this matter has not been studied in a systematic manner. It is therefore unclear how these SFs would perform when only trained on protein-ligand complexes that are highly dissimilar or highly similar to the test set. It is also unclear whether SFs based on machine learning algorithms other than RF can also improve accuracy with increasing training set size and to what extent they learn from dissimilar or similar training complexes. RESULTS: We present a systematic study to investigate how the accuracy of classical and machine-learning SFs varies with protein-ligand complex similarities between training and test sets. We considered three types of similarity metrics, based on the comparison of either protein structures, protein sequences or ligand structures. Regardless of the similarity metric, we found that incorporating a larger proportion of similar complexes to the training set did not make classical SFs more accurate. In contrast, RF-Score-v3 was able to outperform X-Score even when trained on just 32% of the most dissimilar complexes, showing that its superior performance owes considerably to learning from dissimilar training complexes to those in the test set. In addition, we generated the first SF employing Extreme Gradient Boosting (XGBoost), XGB-Score, and observed that it also improves with training set size while outperforming the rest of SFs. Given the continuous growth of training datasets, the development of machine-learning SFs has become very appealing. AVAILABILITY AND IMPLEMENTATION: https://github.com/HongjianLi/MLSF. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

By analyzing the logs of corporate e-mail networks we found a number of patterns, showing how the size of ego-networks of individual employees changes on a day by day basis. We proposed a simple model that adequately describes the observed time dependence of an employee's "social circle". Comparison of experimental data with the theoretical model showed that employees are divided into two groups - with fast and slow changes in their social circles, respectively. We believe that the presence of these groups reflects both project-type and process-type of employees' activities. Comparison of data obtained before and during the global economic crisis has shown that the crisis led to an actual reduction in project-type activities.