Protein stability predictions are becoming essential in medicine to develop novel immunotherapeutic agents and for drug discovery. Despite the large number of computational approaches for predicting the protein stability upon mutation, there are still critical unsolved problems: 1) the limited number of thermodynamic measurements for proteins provided by current databases; 2) the large intrinsic variability of ΔΔG values due to different experimental conditions; 3) biases in the development of predictive methods caused by ignoring the anti-symmetry of ΔΔG values between mutant and native protein forms; 4) over-optimistic prediction performance, due to sequence similarity between proteins used in training and test datasets. Here, we review these issues, highlighting new challenges required to improve current tools and to achieve more reliable predictions. In addition, we provide a perspective of how these methods will be beneficial for designing novel precision medicine approaches for several genetic disorders caused by mutations, such as cancer and neurodegenerative diseases.

In this work the feasibility of near infrared spectroscopy was evaluated combined with chemometric approaches, as a tool for the botanical origin prediction of 119 honey samples. Four varieties related to polyfloral, acacia, chestnut, and linden were first characterized by their physical–chemical parameters and then analyzed in triplicate using a near infrared spectrophotometer equipped with an optical path gold reflector. Three different classifiers were built on distinct multivariate and machine learning approaches for honey botanical classification. A partial least squares discriminant analysis was used as a first approach to build a predictive model for honey classification. Spectra pretreatments named autoscale, standard normal variate, detrending, first derivative, and smoothing were applied for the reduction of scattering related to the presence of particle size, like glucose crystals. The values of the descriptive statistics of the partial least squares discriminant analysis model allowed a sufficient floral group prediction for the acacia and polyfloral honeys but not in the cases of chestnut and linden. The second classifier, based on a support vector machine, allowed a better classification of acacia and polyfloral and also achieved the classification of chestnut. The linden samples instead remained unclassified. A further investigation, aimed to improve the botanical discrimination, exploited a feature selection algorithm named Boruta, which assigned a pool of 39 informative averaged near infrared spectral variables on which a canonical discriminant analysis was assessed. The canonical discriminant analysis accounted a better separation of samples according to the botanical origin than the partial least squares discriminant analysis. The approach used has permitted to achieve a complete authentication of the acacia honeys but not a precise segregation of polyfloral ones. The comparison between the variables important in projection and the Boruta pool showed that the informative wavelengths are partially shared especially in the middle and far band of the near infrared spectral range.

Accurate prediction of protein stability changes upon single-site variations (ΔΔG) is important for protein design, as well as for our understanding of the mechanisms of genetic diseases. The performance of high-throughput computational methods to this end is evaluated mostly based on the Pearson correlation coefficient between predicted and observed data, assuming that the upper bound would be 1 (perfect correlation). However, the performance of these predictors can be limited by the distribution and noise of the experimental data. Here we estimate, for the first time, a theoretical upper-bound to the ΔΔG prediction performances imposed by the intrinsic structure of currently available ΔΔG data. Given a set of measured ΔΔG protein variations, the theoretically “best predictor” is estimated based on its similarity to another set of experimentally determined ΔΔG values. We investigate the correlation between pairs of measured ΔΔG variations, where one is used as a predictor for the other. We analytically derive an upper bound to the Pearson correlation as a function of the noise and distribution of the ΔΔG data. We also evaluate the available datasets to highlight the effect of the noise in conjunction with ΔΔG distribution. We conclude that the upper bound is a function of both uncertainty and spread of the ΔΔG values, and that with current data the best performance should be between 0.7 and 0.8, depending on the dataset used; higher Pearson correlations might be indicative of overtraining. It also follows that comparisons of predictors using different datasets are inherently misleading. Supplementary data are available at Bioinformatics online.

Vertebrate visual phototransduction is perhaps the most well-studied G-protein signaling pathway. A wealth of available biochemical and electrophysiological data has resulted in a rich history of mathematical modeling of the system. However, while the most comprehensive models have relied upon amphibian biochemical and electrophysiological data, modern research typically employs mammalian species, particularly mice, which exhibit significantly faster signaling dynamics. In this work, we present an adaptation of a previously published, comprehensive model of amphibian phototransduction that can produce quantitatively accurate simulations of the murine photoresponse. We demonstrate the ability of the model to predict responses to a wide range of stimuli and under a variety of mutant conditions. Finally, we employ the model to highlight a likely unknown mechanism related to the interaction between rhodopsin and rhodopsin kinase.

Motivation: A basic question in protein science is to which extent mutations affect protein thermostability. This knowledge would be particularly relevant for engineering thermostable enzymes. In several experimental approaches, this issue has been serendipitously addressed. It would be therefore convenient providing a computational method that predicts when a given protein mutant is more thermostable than its corresponding wild-type. Results: We present a new method based on support vector machines that is able to predict whether a set of mutations (including insertion and deletions) can enhance the thermostability of a given protein sequence. When trained and tested on a redundancy-reduced dataset, our predictor achieves 88% accuracy and a correlation coefficient equal to 0.75. Our predictor also correctly classifies 12 out of 14 experimentally characterized protein mutants with enhanced thermostability. Finally, it correctly detects all the 11 mutated proteins whose increase in stability temperature is >10°C. Availability: The dataset and the list of protein clusters adopted for the SVM cross-validation are available at the web site http://lipid.biocomp.unibo.it/~ludovica/thermo-meso-MUT. Contact:casadio@alma.unibo.it