Improving the Prediction of Protein Structural Class for Low-Similarity Sequences by Incorporating Evolutionaryand Structural Information

2016 ◽  
Vol 20 (3) ◽  
pp. 402-411 ◽  
Author(s):  
Liang Kong ◽  
◽  
Lingfu Kong ◽  
Rong Jing ◽  
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Sequence Similarity ◽  
Computational Method ◽  
Evolutionary Information ◽  
Support Vector ◽  
Local Alignment ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class

Protein structural class prediction is beneficial to study protein function, regulation and interactions. However, protein structural class prediction for low-similarity sequences (i.e., below 40% in pairwise sequence similarity) remains a challenging problem at present. In this study, a novel computational method is proposed to accurately predict protein structural class for low-similarity sequences. This method is based on support vector machine in conjunction with integrated features from evolutionary information generated with position specific iterative basic local alignment search tool (PSI-BLAST) and predicted secondary structure. Various prediction accuracies evaluated by the jackknife tests are reported on two widely-used low-similarity benchmark datasets (25PDB and 1189), reaching overall accuracies 89.3% and 87.9%, which are significantly higher than those achieved by state-of-the-art in protein structural class prediction. The experimental results suggest that our method could serve as an effective alternative to existing methods in protein structural classification, especially for low-similarity sequences.

SVM-BASED METHOD FOR PROTEIN STRUCTURAL CLASS PREDICTION USING SECONDARY STRUCTURAL CONTENT AND STRUCTURAL INFORMATION OF AMINO ACIDS

2011 ◽  
Vol 09 (04) ◽  
pp. 489-502 ◽  
Author(s):  
TABREZ ANWAR SHAMIM MOHAMMAD ◽  
HAMPAPATHALU ADIMURTHY NAGARAJARAM
Keyword(s):  
Amino Acids ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Protein Structures ◽  
Classification Problem ◽  
Support Vector ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Structural Content

The knowledge collated from the known protein structures has revealed that the proteins are usually folded into the four structural classes: all-α, all-β, α/β and α + β. A number of methods have been proposed to predict the protein's structural class from its primary structure; however, it has been observed that these methods fail or perform poorly in the cases of distantly related sequences. In this paper, we propose a new method for protein structural class prediction using low homology (twilight-zone) protein sequences dataset. Since protein structural class prediction is a typical classification problem, we have developed a Support Vector Machine (SVM)-based method for protein structural class prediction that uses features derived from the predicted secondary structure and predicted burial information of amino acid residues. The examination of different individual as well as feature combinations revealed that the combination of secondary structural content, secondary structural and solvent accessibility state frequencies of amino acids gave rise to the best leave-one-out cross-validation accuracy of ~81% which is comparable to the best accuracy reported in the literature so far.

Protein Structural Class Prediction Based on Distance-related Statistical Features from Graphical Representation of Predicted Secondary Structure

2019 ◽  
Vol 16 (4) ◽  
pp. 317-324
Author(s):  
Liang Kong ◽  
Lichao Zhang ◽  
Xiaodong Han ◽  
Jinfeng Lv
Keyword(s):  
Feature Extraction ◽  
Secondary Structure ◽  
Protein Sequence ◽  
Function Analysis ◽  
Superior Performance ◽  
Support Vector ◽  
Chaos Game Representation ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class

Protein structural class prediction is beneficial to protein structure and function analysis. Exploring good feature representation is a key step for this prediction task. Prior works have demonstrated the effectiveness of the secondary structure based feature extraction methods especially for lowsimilarity protein sequences. However, the prediction accuracies still remain limited. To explore the potential of secondary structure information, a novel feature extraction method based on a generalized chaos game representation of predicted secondary structure is proposed. Each protein sequence is converted into a 20-dimensional distance-related statistical feature vector to characterize the distribution of secondary structure elements and segments. The feature vectors are then fed into a support vector machine classifier to predict the protein structural class. Our experiments on three widely used lowsimilarity benchmark datasets (25PDB, 1189 and 640) show that the proposed method achieves superior performance to the state-of-the-art methods. It is anticipated that our method could be extended to other graphical representations of protein sequence and be helpful in future protein research.

scholarly journals Protein structural class prediction using predicted secondary structure and hydropathy profile

2021 ◽  
Author(s):  
Syeda Nadia Firdaus
Keyword(s):  
Secondary Structure ◽  
Classification Problem ◽  
Support Vector ◽  
Prediction Problem ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Vector Machines ◽  
Structural Classes ◽  
New Strategies

This thesis explores machine learning models based on various feature sets to solve the protein structural class prediction problem which is a significant classification problem in bioinformatics. Knowledge of protein structural classes contributes to an understanding of protein folding patterns, and this has made structural class prediction research a major topic of interest. In this thesis, features are extracted from predicted secondary structure and hydropathy sequence using new strategies to classify proteins into one of the four major structural classes: all-α, all-β, α/β, and α+β. The prediction accuracy using these features compares favourably with some existing successful methods. We use Support Vector Machines (SVM), since this learning method has well-known efficiency in solving this classification problem. On a standard dataset (25PDB), the proposed system has an overall accuracy of 89% with as few as 22 features, whereas the previous best performing method had an accuracy of 88% using 2510 features.

scholarly journals Recent Advances in the Prediction of Protein Structural Classes: Feature Descriptors and Machine Learning Algorithms

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 324
Author(s):  
Lin Zhu ◽  
Mehdi D. Davari ◽  
Wenjin Li
Keyword(s):  
Machine Learning ◽  
Protein Structure ◽  
Protein Function ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Feature Descriptors ◽  
New Feature

In the postgenomic age, rapid growth in the number of sequence-known proteins has been accompanied by much slower growth in the number of structure-known proteins (as a result of experimental limitations), and a widening gap between the two is evident. Because protein function is linked to protein structure, successful prediction of protein structure is of significant importance in protein function identification. Foreknowledge of protein structural class can help improve protein structure prediction with significant medical and pharmaceutical implications. Thus, a fast, suitable, reliable, and reasonable computational method for protein structural class prediction has become pivotal in bioinformatics. Here, we review recent efforts in protein structural class prediction from protein sequence, with particular attention paid to new feature descriptors, which extract information from protein sequence, and the use of machine learning algorithms in both feature selection and the construction of new classification models. These new feature descriptors include amino acid composition, sequence order, physicochemical properties, multiprofile Bayes, and secondary structure-based features. Machine learning methods, such as artificial neural networks (ANNs), support vector machine (SVM), K-nearest neighbor (KNN), random forest, deep learning, and examples of their application are discussed in detail. We also present our view on possible future directions, challenges, and opportunities for the applications of machine learning algorithms for prediction of protein structural classes.

Development of Novel Multi-Objective Based Model for Protein Structural Class Prediction

2016 ◽  
pp. 76-107 ◽  
Author(s):  
Bishnupriya Panda ◽  
Babita Majhi
Keyword(s):  
Neural Network ◽  
Accurate Determination ◽  
Rational Drug Design ◽  
Computational Method ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Multi Objective ◽  
Representation Method

Protein folding has played a vital role in rational drug design, pharmacology and many other applications. The knowledge of protein structural class provides useful information towards the determination of protein structure. The exponential growth of newly discovered protein sequences by different scientific communities has made a large gap between the number of sequence-known and the number of structure-known proteins. Accurate determination of protein structural class using a suitable computational method has been a challenging problem in protein science. This chapter is based on the concept of Chou's pseudo amino acid composition feature representation method. Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. On the basis of such a statistical framework a low complexity functional link artificial neural network and a complex novel hybrid model using radial basis function neural network and multi-objective algorithm based classifier are introduced to predict protein structural class.

scholarly journals Protein structural class prediction using predicted secondary structure and hydropathy profile

2021 ◽  
Author(s):  
Syeda Nadia Firdaus
Keyword(s):  
Secondary Structure ◽  
Classification Problem ◽  
Support Vector ◽  
Prediction Problem ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Vector Machines ◽  
Structural Classes ◽  
New Strategies

This thesis explores machine learning models based on various feature sets to solve the protein structural class prediction problem which is a significant classification problem in bioinformatics. Knowledge of protein structural classes contributes to an understanding of protein folding patterns, and this has made structural class prediction research a major topic of interest. In this thesis, features are extracted from predicted secondary structure and hydropathy sequence using new strategies to classify proteins into one of the four major structural classes: all-α, all-β, α/β, and α+β. The prediction accuracy using these features compares favourably with some existing successful methods. We use Support Vector Machines (SVM), since this learning method has well-known efficiency in solving this classification problem. On a standard dataset (25PDB), the proposed system has an overall accuracy of 89% with as few as 22 features, whereas the previous best performing method had an accuracy of 88% using 2510 features.

scholarly journals Combination between DE and SVM to enhance Protein Structure Prediction based on Secondary Structural information

2019 ◽  
Vol 8 (4) ◽  
pp. 478
Author(s):  
Thair A. Kadhim ◽  
Mohammed Hasan Aldulaimi ◽  
Suhaila Zainudin ◽  
Azuraliza Abu Bakar
Keyword(s):  
Structure Prediction ◽  
Structural Information ◽  
Accurate Method ◽  
Support Vector ◽  
Svm Classifier ◽  
Classification Rate ◽  
Structural Class ◽  
Protein Structural Class ◽  
Computational Intelligence Methods ◽  
Feature Selection Approach

The effective selection of protein features and the accurate method for predicting protein structural class (PSP) is an important aspect in protein folding, especially for low-similarity sequences. Many promising approaches are proposed to solve this problem, mostly via computational intelligence methods. One of the main aspect of the prediction is the extraction of an excellent representation of a protein sequence. An integrated vector of dimensions 71 was extracted using secondary and hydropathy information in this study Using newly developed strategies for categorizing proteins into their respective main structures classes, which are all-α, all-β, α/β, and α+β. Support Vector Machine (SVM) and Differential Evolution (DE) were combined using the wrapper method to select the top N features based on the level of their respective importance. The classification can be made more accurate by tuning the kernel parameters for the SVM in the training phase. In this study, the mean of the classification rate from using the SVM classifier was used to evaluate the selected subset of features. This study was tested using two low - similarity data sets (D640 and ASTRAL). A comparison between the proposed (SVM + DE) based on DE feature selection approach and (SVM+DE) based on grid search (a traditional method to search for parameters) forms the core of this work. The proposed SVM+DE model is competitive and highly reliable in terms of time and performance accuracy compared with other reported methods in literature.   

scholarly journals An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ji-Yong An ◽  
Fan-Rong Meng ◽  
Zi-Ji Yan
Keyword(s):  
Ion Channel ◽  
Extreme Learning Machine ◽  
Nuclear Receptor ◽  
Drug Target ◽  
Computational Method ◽  
Evolutionary Information ◽  
Support Vector ◽  
Weighted Extreme Learning Machine ◽  
Speed Up ◽  
Learning Machine

Abstract Background Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experimental methods. Therefore, it is a challenging task that how to develop efficient computational approaches for the accurate predicting potential associations between drug and target. Results In the paper, we proposed a novel computational method called WELM-SURF based on drug fingerprints and protein evolutionary information for identifying DTIs. More specifically, for exploiting protein sequence feature, Position Specific Scoring Matrix (PSSM) is applied to capturing protein evolutionary information and Speed up robot features (SURF) is employed to extract sequence key feature from PSSM. For drug fingerprints, the chemical structure of molecular substructure fingerprints was used to represent drug as feature vector. Take account of the advantage that the Weighted Extreme Learning Machine (WELM) has short training time, good generalization ability, and most importantly ability to efficiently execute classification by optimizing the loss function of weight matrix. Therefore, the WELM classifier is used to carry out classification based on extracted features for predicting DTIs. The performance of the WELM-SURF model was evaluated by experimental validations on enzyme, ion channel, GPCRs and nuclear receptor datasets by using fivefold cross-validation test. The WELM-SURF obtained average accuracies of 93.54, 90.58, 85.43 and 77.45% on enzyme, ion channels, GPCRs and nuclear receptor dataset respectively. We also compared our performance with the Extreme Learning Machine (ELM), the state-of-the-art Support Vector Machine (SVM) on enzyme and ion channels dataset and other exiting methods on four datasets. By comparing with experimental results, the performance of WELM-SURF is significantly better than that of ELM, SVM and other previous methods in the domain. Conclusion The results demonstrated that the proposed WELM-SURF model is competent for predicting DTIs with high accuracy and robustness. It is anticipated that the WELM-SURF method is a useful computational tool to facilitate widely bioinformatics studies related to DTIs prediction.

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