Pseudo Position-specific Scoring Matrix Research Articles

DNA protein binding recognition based on lifelong learning

In recent years, research in the field of bioinformatics has focused on predicting the raw sequences of proteins, and some scholars consider DNA-binding protein prediction as a classification task. Many statistical and machine learning-based methods have been widely used in DNA-binding proteins research. The aforementioned methods are indeed more efficient than those based on manual classification, but there is still room for improvement in terms of prediction accuracy and speed. In this study, researchers used Average Blocks, Discrete Cosine Transform, Discrete Wavelet Transform, Global encoding, Normalized Moreau-Broto Autocorrelation and Pseudo position-specific scoring matrix to extract evolutionary features. A dynamic deep network based on lifelong learning architecture was then proposed in order to fuse six features and thus allow for more efficient classification of DNA-binding proteins. The multi-feature fusion allows for a more accurate description of the desired protein information than single features. This model offers a fresh perspective on the dichotomous classification problem in bioinformatics and broadens the application field of lifelong learning. The researchers ran trials on three datasets and contrasted them with other classification techniques to show the model’s effectiveness in this study. The findings demonstrated that the model used in this research was superior to other approaches in terms of single-sample specificity (81.0%, 83.0%) and single-sample sensitivity (82.4%, 90.7%), and achieves high accuracy on the benchmark dataset (88.4%, 80.0%, and 76.6%).

Prediction of protein-protein interactions based on ensemble residual convolutional neural network

With the development of bio-medical big data, the prediction of protein-protein interactions (PPIs) with the help of deep learning (DL) has attracted much attention for the study of intermolecular mechanism, drug design, human disease treatment. Given that the experiment-based methods can be difficult, reliable and DL-based approaches are needed. In this paper, we develop the EResCNN, an effective predictor to predict PPIs based on ensemble residual convolutional neural network. First, the fused feature representation is captured by concatenating the vectors obtained via pseudo amino acid composition (PseAAC), auto covariance descriptor (AC), pseudo position-specific scoring matrix (PsePSSM), encoding based on grouped weight (EBGW), multivariate mutual information (MMI) and conjoint triad (CT). Then the high-level information can be obtained using the convolution and pooling of the residual convolutional neural network (RCNN) via layer-by-layer learning. At last, we ensemble RCNN, XGBoost, random forest, LightGBM and extremely randomized trees to build the EResCNN model. The predictive results indicate that EResCNN achieves better performance with the ACC values of 95.34%, 87.89% and 98.61% on S. cerevisiae, H. pylori and Human-Y. pestis datasets, respectively. We also apply EResCNN to the datasets of H. sapiens, M. musculus, C. elegans and E. coli for cross-species prediction. Especially, we find EResCNN can infer significant PPIs network on one-core network, Wnt-related signal pathway network, cancer-specific network and multi-core network, which could provide some references for signal pathway research, disease-related gene mining, and interaction network topology.

Prediction of antifreeze proteins using machine learning

Living organisms including fishes, microbes, and animals can live in extremely cold weather. To stay alive in cold environments, these species generate antifreeze proteins (AFPs), also referred to as ice-binding proteins. Moreover, AFPs are extensively utilized in many important fields including medical, agricultural, industrial, and biotechnological. Several predictors were constructed to identify AFPs. However, due to the sequence and structural heterogeneity of AFPs, correct identification is still a challenging task. It is highly desirable to develop a more promising predictor. In this research, a novel computational method, named AFP-LXGB has been proposed for prediction of AFPs more precisely. The information is explored by Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Position Specific Scoring Matrix-Segmentation-Autocorrelation Transformation (Sg-PSSM-ACT), and Pseudo Position Specific Scoring Matrix Tri-Slicing (PseTS-PSSM). Keeping the benefits of ensemble learning, these feature sets are concatenated into different combinations. The best feature set is selected by Extremely Randomized Tree-Recursive Feature Elimination (ERT-RFE). The models are trained by Light eXtreme Gradient Boosting (LXGB), Random Forest (RF), and Extremely Randomized Tree (ERT). Among classifiers, LXGB has obtained the best prediction results. The novel method (AFP-LXGB) improved the accuracies by 3.70% and 4.09% than the best methods. These results verified that AFP-LXGB can predict AFPs more accurately and can participate in a significant role in medical, agricultural, industrial, and biotechnological fields.

Identification of Vesicle Transport Proteins via Hypergraph Regularized K-Local Hyperplane Distance Nearest Neighbour Model

The prediction of protein function is a common topic in the field of bioinformatics. In recent years, advances in machine learning have inspired a growing number of algorithms for predicting protein function. A large number of parameters and fairly complex neural networks are often used to improve the prediction performance, an approach that is time-consuming and costly. In this study, we leveraged traditional features and machine learning classifiers to boost the performance of vesicle transport protein identification and make the prediction process faster. We adopt the pseudo position-specific scoring matrix (PsePSSM) feature and our proposed new classifier hypergraph regularized k-local hyperplane distance nearest neighbour (HG-HKNN) to classify vesicular transport proteins. We address dataset imbalances with random undersampling. The results show that our strategy has an area under the receiver operating characteristic curve (AUC) of 0.870 and a Matthews correlation coefficient (MCC) of 0.53 on the benchmark dataset, outperforming all state-of-the-art methods on the same dataset, and other metrics of our model are also comparable to existing methods.

RoFDT: Identification of Drug-Target Interactions from Protein Sequence and Drug Molecular Structure Using Rotation Forest.

As the basis for screening drug candidates, the identification of drug-target interactions (DTIs) plays a crucial role in the innovative drugs research. However, due to the inherent constraints of small-scale and time-consuming wet experiments, DTI recognition is usually difficult to carry out. In the present study, we developed a computational approach called RoFDT to predict DTIs by combining feature-weighted Rotation Forest (FwRF) with a protein sequence. In particular, we first encode protein sequences as numerical matrices by Position-Specific Score Matrix (PSSM), then extract their features utilize Pseudo Position-Specific Score Matrix (PsePSSM) and combine them with drug structure information-molecular fingerprints and finally feed them into the FwRF classifier and validate the performance of RoFDT on Enzyme, GPCR, Ion Channel and Nuclear Receptor datasets. In the above dataset, RoFDT achieved 91.68%, 84.72%, 88.11% and 78.33% accuracy, respectively. RoFDT shows excellent performance in comparison with support vector machine models and previous superior approaches. Furthermore, 7 of the top 10 DTIs with RoFDT estimate scores were proven by the relevant database. These results demonstrate that RoFDT can be employed to a powerful predictive approach for DTIs to provide theoretical support for innovative drug discovery.

IAFPs-EnC-GA: Identifying antifungal peptides using sequential and evolutionary descriptors based multi-information fusion and ensemble learning approach

Fungal infections have become a serious health concern for human beings worldwide. Fungal infections usually occur when the invading fungus appear on a particular part of the body and become hard for the human immune system to resist. The existing antifungal treatments are considered inappropriate because of their severe side effects. With the rapid growth of this chronic disease across the world, an accurate prediction model for fungal infections has become a challenging task for scientists. To cope with these issues, several prediction methods have been established for antifungal peptides. However, due to the limited and unsatisfactory performance of these methods, it is still highly indispensable to develop an effective and reliable model of antifungal peptides. In this study, we present an intelligent learning approach for the accurate prediction of antifungal peptides. The sequential and evolutionary features are explored by three promising descriptors namely conjoint triad feature (CTF), Pseudo-position specific scoring matrix (PsePSSM), and Position-specific scoring matrix-Discrete wavelet transform (PSSM-DWT). Moreover, the extracted vectors of the encoding methods are then fused to get multi-perspective descriptors representing both sequential and evolutionary features. In addition, to reduce the size of the multi-information vector and to eradicate noisy and irrelevant descriptors, we applied minimum redundancy and maximum relevance (mRMR) based feature selection to choose the optimal feature set. In the next step, the selected feature vector is evaluated via four different machine learning models, i.e. Fuzzy K-nearest neighbor (FKNN), Random Forest (RF),k-nearest neighbor (KNN), and Support Vector Machine (SVM). In addition, the predicted labels of the individual learning algorithms are then provided to the genetic algorithm to form an ensemble classifier to further boost the prediction results. Furthermore, the SHAP and LIME methods were used to interpret the contribution of features to model predictions. Our proposed iAFPs-EnC-GA model achieved a higher prediction accuracy of 97.81% and 93.92% using training and independent datasets, respectively. Which is ∼4% higher than existing models. It is suggested that the “iAFPs-EnC-GA” model will be a valuable tool for scientists and might play a key role in drug development and academic research. The source code and all datasets are publicly available at https://github.com/farmanit335/iAFPs-EnC-GA.

DeepStack-DTIs: Predicting Drug–Target Interactions Using LightGBM Feature Selection and Deep-Stacked Ensemble Classifier

Accurate prediction of drug-target interactions (DTIs), which is often used in the fields of drug discovery and drug repositioning, is regarded a key challenge in the study of drug science. In this paper, a new method called DeepStack-DTIs is proposed to predict DTIs. First, for the target protein, pseudo-positionspecific score matrix, pseudo amino acid composition and SPIDER3 are used to extract the different feature information of the target protein. Meanwhile, the path-based fingerprint features of each drug are extracted. Then, the synthetic minority oversampling technique (SMOTE) and light gradient boosting machine (LightGBM) are used for data balancing and feature selection, respectively. Finally, the processed features are input to the deep-stacked ensemble classifier composed of gated recurrent unit (GRU), deep neural network (DNN), support vector machine (SVM), eXtreme gradient boosting (XGBoost) and logistic regression (LR) to predict DTIs. Under the five-fold cross-validation and compared with existing methods, the proposed method achieves higher prediction accuracy on the gold standard dataset. To evaluate the predictive power of DeepStack-DTIs, we validate the method on another dataset and predict the drug-target interaction network. The results indicate that DeepStack-DTIs has excellent predictive ability than the other methods, and provides novel insights for the prediction of DTIs. A novel method DeepStack-DTIs for drug-target interactions prediction. PsePSSM, PseAAC, SPIDER3 and FP2 are fused to convert protein sequence and drug molecule information into digital information, respectively. The SMOTE algorithm is used to balance the dataset and LightGBM feature selection algorithm is employed to remove redundant and irrelevant features to select the optimal feature subset. This optimal feature subset is inputted into the deep-stacked ensemble classifier to predict drug-target interactions. The experimental results show DeepStack-DTIs method can significantly improve the prediction accuracy of drug-target interactions.

DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network.

Analysis and prediction of drug-target interactions (DTIs) play an important role in understanding drug mechanisms, as well as drug repositioning and design. Machine learning (ML)-based methods for DTIs prediction can mitigate the shortcomings of time-consuming and labor-intensive experimental approaches, while providing new ideas and insights for drug design. We propose a novel pipeline for predicting drug-target interactions, called DNN-DTIs. First, the target information is characterized by a number of features, namely, pseudo-amino acid composition, pseudo position-specific scoring matrix, conjoint triad composition, transition and distribution, Moreau-Broto autocorrelation, and structural features. The drug compounds are subsequently encoded using substructure fingerprints. Next, eXtreme gradient boosting (XGBoost) is used to determine the subset of non-redundant features of importance. The optimal balanced set of sample vectors is obtained by applying the synthetic minority oversampling technique (SMOTE). Finally, a DTIs predictor, DNN-DTIs, is developed based on a deep neural network (DNN) via a layer-by-layer learning scheme. Experimental results indicate that DNN-DTIs achieves better performance than other state-of-the-art predictors with ACC values of 98.78%, 98.60%, 97.98%, 98.24% and 98.00% on Enzyme, Ion Channels (IC), GPCR, Nuclear Receptors (NR) and Kuang's datasets. Therefore, the accurate prediction performance of DNN-DTIs makes it a favored choice for contributing to the study of DTIs, especially drug repositioning.

Prediction of protein-protein interaction sites through eXtreme gradient boosting with kernel principal component analysis

Predicting protein-protein interaction sites (PPI sites) can provide important clues for understanding biological activity. Using machine learning to predict PPI sites can mitigate the cost of running expensive and time-consuming biological experiments. Here we propose PPISP-XGBoost, a novel PPI sites prediction method based on eXtreme gradient boosting (XGBoost). First, the characteristic information of protein is extracted through the pseudo-position specific scoring matrix (PsePSSM), pseudo-amino acid composition (PseAAC), hydropathy index and solvent accessible surface area (ASA) under the sliding window. Next, these raw features are preprocessed to obtain more optimal representations in order to achieve better prediction. In particular, the synthetic minority oversampling technique (SMOTE) is used to circumvent class imbalance, and the kernel principal component analysis (KPCA) is applied to remove redundant characteristics. Finally, these optimal features are fed to the XGBoost classifier to identify PPI sites. Using PPISP-XGBoost, the prediction accuracy on the training dataset Dset186 reaches 85.4%, and the accuracy on the independent validation datasets Dtestset72, PDBtestset164, Dset_448 and Dset_355 reaches 85.3%, 83.9%, 85.8% and 85.4%, respectively, which all show an increase in accuracy against existing PPI sites prediction methods. These results demonstrate that the PPISP-XGBoost method can further enhance the prediction of PPI sites.

Accurate prediction of multi-label protein subcellular localization through multi-view feature learning with RBRL classifier.

Multi-label proteins can participate in carrier transportation, enzyme catalysis, hormone regulation and other life activities. Meanwhile, they play a key role in the fields of biopharmaceuticals, gene and cell therapy. This article proposes a prediction method called Mps-mvRBRL to predict the subcellular localization (SCL) of multi-label protein. Firstly, pseudo position-specific scoring matrix, dipeptide composition, position specific scoring matrix-transition probability composition, gene ontology and pseudo amino acid composition algorithms are used to obtain numerical information from different views. Based on the contribution of five individual feature extraction methods, differential evolution is used for the first time to learn the weight of single feature, and then these original features use a weighted combination method to fuse multi-view information. Secondly, the fused high-dimensional features use a weighted linear discriminant analysis framework based on binary weight form to eliminate irrelevant information. Finally, the best feature vector is input into the joint ranking support vector machine and binary relevance with robust low-rank learning classifier to predict the SCL. After applying leave-one-out cross-validation, the overall actual accuracy (OAA) and overall location accuracy (OLA) of Mps-mvRBRL on the training set of Gram-positive bacteria are both 99.81%. The OAA on the test sets of plant, virus and Gram-negative bacteria datasets are 97.24%, 98.55% and 98.20%, respectively, and the OLA are 97.16%, 97.62% and 98.28%, respectively. The results show that the model achieves good prediction performance for predicting the SCL of multi-label protein.

Feature Based Method for Predicting Pharmacological Interaction

Prediction of drug target interaction is an extrusive domain of drug discovery and repositioning of drugs. Most conventional studies are carried out in early years in the wet laboratory, but it is very expensive and time consuming. So nowadays, the use of machine learning techniques to predict drug target pairs. A new method of interaction targeting drugs is introduced in this paper. Use the Pseudo Position Specific Scoring Matrix (PsePSSM) is used to represent the target, which generate features that describe the original information of protein. The drug chemical structure information can be extracted through FP2 molecular fingerprint which describe the molecular structure information. Then a drug target interaction network is constructed using bipartite graph where in which each node represents a target or drug and each link indicates a drug target interaction. From the above stages, the data contains some noise and redundant data which have a negative impact on the prediction output. So, LASSO (Least Absolute Shrinkage and Selection Operator) method is handle it and reduce the dimension of the extracted feature information of original data. But drug target pair samples have some imbalanced, then cost-sensitive ensemble method is used to address the imbalanced problem between positive and negative samples, and learns about the minority class by assigning higher costs and optimizing their cost error. Finally, the processed data is given as input to the extreme gradient boosting classifier algorithm for predicting new drug target interaction pairs. This method can significantly improve the prediction accuracy of drug target interaction.

MpsLDA-ProSVM: Predicting multi-label protein subcellular localization by wMLDAe dimensionality reduction and ProSVM classifier

Multi-label proteins play a significant role in life processes such as cell growth, development, and reproduction. Exploring protein subcellular localization (SCL) is a direct way to better understand the function of multi-label proteins in cells. This paper firstly presents a new prediction model named MpsLDA-ProSVM which predicts the SCL of multi-label proteins. Firstly, we utilize four coding algorithms including pseudo position-specific scoring matrix (PsePSSM), gene ontology (GO), conjoint triad (CT) and pseudo amino acid composition (PseAAC) to draw the feature information from protein sequences. Then, for the first time, we use a weighted multi-label linear discriminant analysis framework based on entropy weight form (wMLDAe) to refine and purify features. Finally, we input the optimal feature subset into the multi-label learning with label-specific features (LIFT) and multi-label k-nearest neighbor (ML-KNN) algorithms to obtain a synthetic ranking of relevant labels, and then use Prediction and Relevance Ordering based SVM (ProSVM) classifier to predict the SCLs. Tested by leave-one-out cross-validation (LOOCV), the overall actual accuracy on virus, plant, Gram-positive bacteria and Gram-negative bacteria datasets are 98.06%, 98.97%, 99.81% and 98.49%, which are 0.56%–9.16%, 1.07%–30.87%, 0.21%–6.91% and 3.99%–8.59% higher than other advanced methods respectively. By comparison, the model MpsLDA-ProSVM can effectively predict the specific location of multi-label proteins in cells.

GTB-PPI: Predict Protein–protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting

Protein–protein interactions (PPIs) are of great importance to understand genetic mechanisms, delineate disease pathogenesis, and guide drug design. With the increase of PPI data and development of machine learning technologies, prediction and identification of PPIs have become a research hotspot in proteomics. In this study, we propose a new prediction pipeline for PPIs based on gradient tree boosting (GTB). First, the initial feature vector is extracted by fusing pseudo amino acid composition (PseAAC), pseudo position-specific scoring matrix (PsePSSM), reduced sequence and index-vectors (RSIV), and autocorrelation descriptor (AD). Second, to remove redundancy and noise, we employ L1-regularized logistic regression (L1-RLR) to select an optimal feature subset. Finally, GTB-PPI model is constructed. Five-fold cross-validation showed that GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori datasets, respectively. In addition, GTB-PPI could be applied to predict the independent test datasets for Caenorhabditis elegans, Escherichia coli, Homo sapiens, and Mus musculus, the one-core PPI network for CD9, and the crossover PPI network for the Wnt-related signaling pathways. The results show that GTB-PPI can significantly improve accuracy of PPI prediction. The code and datasets of GTB-PPI can be downloaded from https://github.com/QUST-AIBBDRC/GTB-PPI/.

DMLDA-LocLIFT: Identification of multi-label protein subcellular localization using DMLDA dimensionality reduction and LIFT classifier

Multi-label proteins occur in two or more subcellular locations, which play a vital role in cell development and metabolism. Prediction and analysis of multi-label subcellular localization (SCL) can present new perspective with drug target identification and new drug design. However, the prediction of multi-label protein SCL using biological experiments is expensive and labor-intensive. Therefore, predicting large-scale SCL with machine learning methods has turned into a popular study topic in bioinformatics. In this study, a novel multi-label learning methods for protein SCL prediction, called DMLDA-LocLIFT, is proposed. Firstly, the dipeptide composition (DC), encoding based on grouped weight (EBGW), pseudo amino acid composition (PseAAC), gene ontology (GO) and pseudo-position specific scoring matrix (PsePSSM) are employed to encode subcellular protein sequences. Then, using direct multi-label linear discriminant analysis (DMLDA) to get rid of noise information of the fused feature vector. Lastly, the first-best feature vectors are input into the multi-label learning with Label-specIfic FeaTures (LIFT) classifier to predict. The leave-one-out cross validation (LOOCV) shows that the overall actual accuracy on Gram-negative bacteria, Gram-positive bacteria, plant datasets, virus dataset and human dataset are 98.6%, 99.6%, 97.9%, 94.7% and 96.1% respectively, which are obviously better than other state-of-the-art prediction methods. The proposed model can effectively predict SCL of multi-label proteins and provide references for experimental identification of SCL. The source codes and datasets are available at https://github.com/QUST-AIBBDRC/DMLDA-LocLIFT/.

Prediction of protein crotonylation sites through LightGBM classifier based on SMOTE and elastic net

Lysine crotonylation is an important protein post-translational modification, which plays an important role in the process of chromosome organization and nucleic acid metabolism. Recognition of crotonylation sites is important to understand the function and mechanism of proteins. Traditional experimental methods are time-consuming and expensive, and can't predict crotonylation sites quickly and accurately. Therefore, this paper proposes a novel crotonylation sites prediction method called LightGBM-CroSite. First, binary encoding (BE), position weight amino acid composition (PWAA), encoding based on grouped weight (EBGW), k nearest neighbors (KNN), pseudo-position specific scoring matrix (PsePSSM) are used to extract features of protein sequences and obtain the original feature space. Second, the elastic net is used to remove redundant information and select the optimal feature subset. Third, the synthetic minority oversampling technique (SMOTE) is used to balance the samples. Finally, the balanced feature vectors are input into LightGBM to predict the crotonylation sites. According to the result of jackknife test, the Accuracy (ACC), Matthew's correlation coefficient (MCC) and area under ROC curve (AUC) are 98.99%, 0.9798 and 0.9996, respectively. Compared with other state-of-the-art methods, the results show that our method has a better model performance on the crotonylation sites prediction. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/LightGBM-CroSite/.

IHBP-DeepPSSM: Identifying hormone binding proteins using PsePSSM based evolutionary features and deep learning approach

Hormone binding proteins (HBPs) are soluble carrier proteins that can non-covalently and selectively interact with the human hormone. HBPs plays a significant role in human life, but its functions are still unclear. Conventional experimental approaches are deemed ineffective due to its high time processing time and cost. Due to the rapid increases in protein sequences, truly characterization of HBPs has become a challenging task for investigators. Measuring the effectiveness of HBPs on the human body, an accurate and reliable intelligent model is desirable for the identification of hormone-binding proteins. In this paper, high discriminative evolutionary features are extracted using a position-specific scoring matrix (PSSM) and Pseudo position-specific scoring matrix (PsePSSM). On the other hand, to reflect the intrinsic correlation and sequence order information, Series Correlation Pseudo Amino Acid Composition (SC-PseAAC) is also applied. Furthermore, to reduce the computational time and to eradicate irreverent and noisy features, the Sequential forward selection and Support Vector Machine (SFS-SVM) based ensemble approach is applied to select optimal features. Furthermore, various diverse nature of learning algorithms is utilized to select the best operational engine for our proposed model. After evaluating the empirical outcomes, deep neural network using optimal PsePSSM features obtained remarkable results. Whereas, our proposed iHBP-DeepPSSM achieved an accuracy of 94.41%, 92.31%, and 90.48% using the training dataset, and independent datasets (S2 and S3), respectively. It is observed that iHBP-DeepPSSM shows an outstanding improvement compared to literature methods. It is expected that the developed model may be played a useful role in research academia as well as proteomics and drug development. The source code and all datasets are publicly available at https://www.github.com/salman-khan-mrd/iHBP-DeepPSSM

SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting

Protein cysteine S-sulfenylation is an essential and reversible post-translational modification that plays a crucial role in transcriptional regulation, stress response, cell signaling and protein function. Studies have shown that S-sulfenylation is involved in many human diseases such as cancer, diabetes and arteriosclerosis. However, experimental identification of protein S-sulfenylation sites is generally expensive and time-consuming. In this study, we proposed a new protein S-sulfenylation sites prediction method SulSite-GTB. First, fusion of amino acid composition, dipeptide composition, encoding based on grouped weight, K nearest neighbors, position-specific amino acid propensity, position-weighted amino acid composition and pseudo-position specific score matrix feature extraction to obtain the initial feature space. Secondly, we use the synthetic minority oversampling technique (SMOTE) algorithm to process the class imbalance data, and the least absolute shrinkage and selection operator (LASSO) are employed to remove the redundant and irrelevant features. Finally, the optimal feature subset is input into the gradient tree boosting classifier to predict the S-sulfenylation sites, and the five-fold cross-validation and independent test set method are used to evaluate the prediction performance of the model. Experimental results showed the overall prediction accuracy is 92.86% and 88.53%, respectively, and the AUC values are 0.9706 and 0.9425, respectively, on the training set and the independent test set. Compared with other prediction methods, the results show that the proposed method SulSite-GTB is significantly superior to other state-of-the-art methods and provides a new idea for the prediction of post-translational modification sites of other proteins. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/SulSite-GTB/ .

Prediction of Extracellular Matrix Proteins by Fusing Multiple Feature Information, Elastic Net, and Random Forest Algorithm

Extracellular matrix (ECM) proteins play an important role in a series of biological processes of cells. The study of ECM proteins is helpful to further comprehend their biological functions. We propose ECMP-RF (extracellular matrix proteins prediction by random forest) to predict ECM proteins. Firstly, the features of the protein sequence are extracted by combining encoding based on grouped weight, pseudo amino-acid composition, pseudo position-specific scoring matrix, a local descriptor, and an autocorrelation descriptor. Secondly, the synthetic minority oversampling technique (SMOTE) algorithm is employed to process the class imbalance data, and the elastic net (EN) is used to reduce the dimension of the feature vectors. Finally, the random forest (RF) classifier is used to predict the ECM proteins. Leave-one-out cross-validation shows that the balanced accuracy of the training and testing datasets is 97.3% and 97.9%, respectively. Compared with other state-of-the-art methods, ECMP-RF is significantly better than other predictors.

DP-BINDER: machine learning model for prediction of DNA-binding proteins by fusing evolutionary and physicochemical information.

DNA-binding proteins (DBPs) participate in various biological processes including DNA replication, recombination, and repair. In the human genome, about 6-7% of these proteins are utilized for genes encoding. DBPs shape the DNA into a compact structure known chromatin while some of these proteins regulate the chromosome packaging and transcription process. In the pharmaceutical industry, DBPs are used as a key component of antibiotics, steroids, and cancer drugs. These proteins also involve in biophysical, biological, and biochemical studies of DNA. Due to the crucial role in various biological activities, identification of DBPs is a hot issue in protein science. A series of experimental and computational methods have been proposed, however, some methods didn't achieve the desired results while some are inadequate in its accuracy and authenticity. Still, it is highly desired to present more intelligent computational predictors. In this work, we introduce an innovative computational method namely DP-BINDER based on physicochemical and evolutionary information. We captured local highly decisive features from physicochemical properties of primary protein sequences via normalized Moreau-Broto autocorrelation (NMBAC) and evolutionary information by position specific scoring matrix-transition probability composition (PSSM-TPC) and pseudo-position specific scoring matrix (PsePSSM) using training and independent datasets. The optimal features were selected by the support vector machine-recursive feature elimination and correlation bias reduction (SVM-RFE + CBR) from fused features and were fed into random forest (RF) and support vector machine (SVM). Our method attained 92.46% and 89.58% accuracy with jackknife and ten-fold cross-validation, respectively on the training dataset, while 81.17% accuracy on the independent dataset for prediction of DBPs. These results demonstrate that our method attained the highest success rate in the literature. The superiority of DP-BINDER over existing approaches due to several reasons including abstraction of local dominant features via effective feature descriptors, utilization of appropriate feature selection algorithms and effective classifier.

CrystalM: A Multi-View Fusion Approach for Protein Crystallization Prediction.

Improving the accuracy of predicting protein crystallization is very important for protein crystallization projects, which is a critical step for the determination of protein structure by X-ray crystallography. At present, many machine learning methods are used to predict protein crystallization. Here, we use a novel feature combination to construct a SVM model in the prediction of protein crystallization, called as CrystalM. In this work, we extract six features to represent protein sequences, namely Average Block-Position specific scoring matrix (AVBlock-PSSM), Average Block-Secondary Structure (AVBlock-SS), Global Encoding (GE), Pseudo-Position specific scoring matrix (PsePSSM), Protscale, and Discrete Wavelet Transform-Position specific scoring matrix (DWT-PSSM). Moreover, we employ two training datasets (TRAIN3587 and TRAIN1500) and their corresponding independent test datasets (TEST3585 and TEST500) to evaluate CrystalM by feeding multi-view features into Support Vector Machine (SVM) classifier. Two training datasets are employed for five-fold cross validation, and two test datasets are separately used to test the corresponding datasets. Finally, we compare CrystalM with other existing methods in the performance. For the datasets of TRAIN3587 and TEST3585, CrystalM achieves best Accuracy (ACC), best Specificity (SP), and the same Mathew's correlation coefficient (MCC) as the previous outperforming methods in the five-fold cross validation. In particular, ACC, SP, and MCC have surpassed the existing methods in independent test, which proves the effectiveness of CrystalM. Meanwhile, ACC, SP, and MCC are higher than existing methods in the five-fold cross validation for TRAIN1500. Although the performance of independent test for TEST500 is not the best, CrystalM also has a certain predictability in the prediction of protein crystallization. In addition, we find that only choosing the first four features can improve the performance of prediction for TRAIN1500 and TEST500, not only in independent tests but also in five-fold cross validation. This phenomenon indicates that the latter two features can not effectively represent proteins of TRAIN1500 and TEST500. CrystalM is a sequence-based protein crystallization prediction method. The good performance on the datasets proves the effectiveness of CrystalM and the better performance on large datasets further demonstrates the stability and superiority of CrystalM.