Phenotypic screenings are usually combined with deconvolution techniques to characterize the mechanism of action for the retrieved hits. These studies can be supported by various computational analyses, although docking simulations are rarely employed. The present study aims to assess if multiple docking calculations can prove successful in target prediction. In detail, the docking simulations submitted to the MEDIATE initiative are utilized to predict the viral targets involved in the hits retrieved by a recently published cytopathic screening. Multiple docking results are combined by the EFO approach to develop target-specific consensus models. The combination of multiple docking simulations enhances the performances of the developed consensus models (average increases in EF1% value of 40% and 25% when combining three and two docking runs, respectively). These models are able to propose reliable targets for about half of the retrieved hits (31 out of 59). Thus, the study emphasizes that docking simulations might be effective in target identification and provide a convincing validation for the collaborative strategies that inspire the MEDIATE initiative. Disappointingly, cross-target and cross-program correlations suggest that common scoring functions are not specific enough for the simulated target.

Near infrared spectroscopy combined with chemometrics was investigated for the fast determination of total organic carbon (TOC) and soluble solids contents (SSC) of Tanreqing injection intermediates. The NIR spectra were collected in transflective mode, and the TOC and SSC reference values were determined with Multi N/C UV HS analyzer and loss on drying method. The samples were divided into calibration sets and validation sets using the Kennard-Stone (KS) algorithm. The Dixon test, leverage and studentized residual test were studied for the sample outlier analysis. The selection of wavebands, spectra pretreated method and the number of latent variables were optimized to obtain better results. The quantitative calibration models were established with 3 different PLS regression algorithms, named linear PLS, non-linear PLS and concentration weighted PLS, and the net result was defined as the average of the predicted values of the different calibration models. The overall results indicated that the presented method is more powerful than single multivariable regression method, characterized by higher mean recovery rate (MRR) of the validation set, and can be used for the rapid determination of TOC and SSC values of Tanreqing injection intermediates, which are two important quality indicators for the process monitoring.

Distributed state estimation plays a key role in space situation awareness via a sensor network. This paper proposes two adaptive consensus-based unscented information filters for tracking target with maneuver and colored measurement noise. The proposed filters can fulfill the distributed estimation for non-linear systems with the aid of a consensus strategy, and can reduce the impact of colored measurement noise by employing the state augmentation and measurement differencing methods. In addition, a fading factor that shrinks the predicted information state and information matrix can suppress the impact of dynamical model error induced by target maneuvers. The performances of the proposed algorithms are investigated by considering a target tracking problem using a space-based radar network. This shows that the proposed algorithms outperform the traditional consensus-based distributed state estimation method in aspects of tracking stability and accuracy.

In the quantitative analysis of spectral data, small sample size and high dimensionality of spectral variables often lead to poor accuracy of a calibration model. We proposed two methods, namely sample consensus and unsupervised variable consensus models, in order to solve the problem of poor accuracy. Three public near-infrared (NIR) or infrared (IR) spectroscopy data from corn, wine, and soil were used to build the partial least squares regression (PLSR) model. Then, Monte Carlo sampling and unsupervised variable clustering methods of a self-organizing map were coupled with the consensus modeling strategy to establish the multiple sub-models. Finally, sample consensus and unsupervised variable consensus models were obtained by assigning the weights to each PLSR sub-model. The calculated results show that both sample consensus and unsupervised variable consensus models can significantly improve the accuracy of the calibration model compared to the single PLSR model. The effectiveness of these two methods points out a new approach to achieve a further accurate result, which can take full advantage of the sample information and valid variable information.

The study proposes a novel consensus strategy based on linear combinations of different docking scores to be used in the evaluation of virtual screening campaigns. The consensus models are generated by applying the recently proposed Enrichment Factor Optimization (EFO) method, which develops the linear equations by exhaustively combining the available docking scores and by optimizing the resulting enrichment factors. The performances of such a consensus strategy were evaluated by simulating the entire Directory of Useful Decoys (DUD datasets). In detail, the poses were initially generated by the PLANTS docking program and then rescored by ReScore+ with and without the minimization of the complexes. The so calculated scores were then used to generate the mentioned consensus models including two or three different scoring functions. The reliability of the generated models was assessed by a per target validation as performed by default by the EFO approach. The encouraging performances of the here proposed consensus strategy are emphasized by the average increase of the 17% in the Top 1% enrichment factor (EF) values when comparing the single best score with the linear combination of three scores. Specifically, kinases offer a truly convincing demonstration of the efficacy of the here proposed consensus strategy since their Top 1% EF average ranges from 6.4 when using the single best performing primary score to 23.5 when linearly combining scoring functions. The beneficial effects of this consensus approach are clearly noticeable even when considering the entire DUD datasets as evidenced by the area under the curve (AUC) averages revealing a 14% increase when combining three scores. The reached AUC values compare very well with those reported in literature by an extended set of recent benchmarking studies and the three-variable models afford the highest AUC average.

The prediction of domain/linker residues in protein sequences is a crucial task in the functional classification of proteins, homology-based protein structure prediction, and high-throughput structural genomics. In this work, a novel consensus-based machine-learning technique was applied for residue-level prediction of the domain/linker annotations in protein sequences using ordered/disordered regions along protein chains and a set of physicochemical properties. Six different classifiers-decision tree, Gaussian naïve Bayes, linear discriminant analysis, support vector machine, random forest, and multilayer perceptron-were exhaustively explored for the residue-level prediction of domain/linker regions. The protein sequences from the curated CATH database were used for training and cross-validation experiments. Test results obtained by applying the developed PDP-CON tool to the mutually exclusive, independent proteins of the CASP-8, CASP-9, and CASP-10 databases are reported. An n-star quality consensus approach was used to combine the results yielded by different classifiers. The average PDP-CON accuracy and F-measure values for the CASP targets were found to be 0.86 and 0.91, respectively. The dataset, source code, and all supplementary materials for this work are available at https://cmaterju.org/cmaterbioinfo/ for noncommercial use.