Machine-Learning-Assisted Rational Design of Si─Rhodamine as Cathepsin-pH-Activated Probe for Accurate Fluorescence Navigation.

High-performance fluorescent probes stand as indispensable tools in fluorescence-guided imaging, and are crucial for precise delineation of focal tissue while minimizing unnecessary removal of healthy tissue. Herein, machine-learning-assisted strategy to investigate the current available xanthene dyes is first proposed, and a quantitative prediction model to guide the rational synthesis of novel fluorescent molecules with the desired pH responsivity is constructed. Two novel Si─rhodamine derivatives are successfully achieved and the cathepsin/pH sequentially activated probe Si─rhodamine─cathepsin-pH (SiR─CTS-pH) is constructed. The results reveal that SiR─CTS-pH exhibits higher signal-to-noise ratio of fluorescence imaging, compared to single pH or cathepsin-activated probe. Moreover, SiR─CTS-pH shows strong differentiation abilities for tumor cells and tissues and accurately discriminates the complex hepatocellular carcinoma tissues from normal ones, indicating its significant application potential in clinical practice. Therefore, the continuous development of xanthene dyes and the rational design of superior fluorescent molecules through machine-learning-assisted model broaden the path and provide more advanced methods to researchers.

Using the augmented Chou's pseudo amino acid composition for predicting protein submitochondria locations based on auto covariance approach.

The submitochondria location of a mitochondrial protein is very important for further understanding the structure and function of this protein. Hence, it is of great practical significance to develop an automated and reliable method for timely identifying the submitochondria locations of novel mitochondrial proteins. In this study, a sequence-based algorithm combining the augmented Chou's pseudo amino acid composition (Chou's PseAA) based on auto covariance (AC) is developed to predict protein submitochondria locations and membrane protein types in mitochondria inner membrane. The model fully considers the sequence-order effects between residues a certain distance apart in the sequence by AC combined with eight representative descriptors for both common proteins and membrane proteins. As a result of jackknife cross-validation tests, the method for submitochondria location prediction yields the accuracies of 91.8%, 96.4% and 66.1% for inner membrane, matrix, and outer membrane, respectively. The total accuracy is 89.7%. When predicting membrane protein types in mitochondria inner membrane, the method achieves the prediction performance with the accuracies of 98.4%, 64.3% and 86.7% for multi-pass inner membrane, single-pass inner membrane, and matrix side inner membrane, where the total accuracy is 93.6%. The overall performance of our method is better than the achievements of the previous studies. So our method can be an effective supplementary tool for future proteomics studies. The prediction software and all data sets used in this article are freely available at http://chemlab.scu.edu.cn/Predict_subMITO/index.htm.

Prediction of neurotoxins by support vector machine based on multiple feature vectors.

Neurotoxin is a toxin which acts on nerve cells by interacting with membrane proteins. Different neurotoxins have different functions and sources. With much more knowledge of neurotoxins it would be greatly helpful for the development of drug design. The support vector machine (SVM) was used to predict the neurotoxin based on multiple feature vector descriptors, including the amino acid composition, length of the protein sequence, weight of the protein and the evolution information described by position specific scoring matrix (PSSM). After a five-fold cross-validation procedure, the method achieved an accuracy of 100% in discriminating neurotoxins from non-toxins. As for classifying neurotoxins based on their sources and functions, the accuracy was 99.50% and 99.38% respectively. At last, the method yielded a good performance in sub-classification of ion channels inhibitors with the total accuracy of 87.27%. These results indicate that this method outperforms previously described NTXpred method.

Local sequence information-based support vector machine to classify voltage-gated potassium channels.

In our previous work, we developed a computational tool, PreK-ClassK-ClassKv, to predict and classify potassium (K+) channels. For K+ channel prediction (PreK) and classification at family level (ClassK), this method performs well. However, it does not perform so well in classifying voltage-gated potassium (Kv) channels (ClassKv). In this paper, a new method based on the local sequence information of Kv channels is introduced to classify Kv channels. Six transmembrane domains of a Kv channel protein are used to define a protein, and the dipeptide composition technique is used to transform an amino acid sequence to a numerical sequence. A Kv channel protein is represented by a vector with 2000 elements, and a support vector machine algorithm is applied to classify Kv channels. This method shows good performance with averages of total accuracy (Acc), sensitivity (SE), specificity (SP), reliability (R) and Matthews correlation coefficient (MCC) of 98.0%, 89.9%, 100%, 0.95 and 0.94 respectively. The results indicate that the local sequence information-based method is better than the global sequence information-based method to classify Kv channels.

Fast fourier transform-based support vector machine for prediction of G-protein coupled receptor subfamilies.

Although the sequence information on G-protein coupled receptors (GPCRs) continues to grow, many GPCRs remain orphaned (i.e. ligand specificity unknown) or poorly characterized with little structural information available, so an automated and reliable method is badly needed to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine has been developed for predicting GPCR subfamilies according to protein's hydrophobicity. In classifying Class B, C, D and F subfamilies, the method achieved an overall Matthe's correlation coefficient and accuracy of 0.95 and 93.3%, respectively, when evaluated using the jackknife test. The method achieved an accuracy of 100% on the Class B independent dataset. The results show that this method can classify GPCR subfamilies as well as their functional classification with high accuracy. A web server implementing the prediction is available at http://chem.scu.edu.cn/blast/Pred-GPCR.