scholarly journals ACT-SVM: Prediction of Protein-Protein Interactions Based on Support Vector Basis Model

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Wenzheng Ma ◽  
Yi Cao ◽  
Wenzheng Bao ◽  
Bin Yang ◽  
Yuehui Chen
Keyword(s):  
Protein Interactions ◽  
Prediction Accuracy ◽  
Support Vector ◽  
Svm Classifier ◽  
Protein Protein Interactions ◽  
Svm Model ◽  
Novel Method ◽  
H Pylori ◽  
Almost All ◽  
Human Dataset

The interactions between proteins play important roles in several organisms, and such issue can be involved in almost all activities in the cell. The research of protein-protein interactions (PPIs) can make a huge contribution to the prevention and treatment of diseases. Currently, many prediction methods based on machine learning have been proposed to predict PPIs. In this article, we propose a novel method ACT-SVM that can effectively predict PPIs. The ACT-SVM model maps protein sequences to digital features, performs feature extraction twice on the protein sequence to obtain vector A and descriptor CT, and combines them into a vector. Then, the feature vectors of the protein pair are merged as the input of the support vector machine (SVM) classifier. We utilize nonredundant H. pylori and human dataset to verify the prediction performance of our method. Finally, the proposed method has a prediction accuracy of 0.727897 for H. pylori data and a prediction accuracy of 0.838799 for human dataset. The results demonstrate that this method can be called a stable and reliable prediction model of PPIs.

INFERRING PROTEIN-PROTEIN INTERACTIONS FROM MESSENGER RNA EXPRESSION PROFILES WITH SVM

2005 ◽  
Vol 13 (03) ◽  
pp. 287-298 ◽  
Author(s):  
JUN CAI ◽  
YING HUANG ◽  
LIANG JI ◽  
YANDA LI
Keyword(s):  
High Throughput ◽  
Protein Interactions ◽  
Messenger Rna ◽  
Expression Profiles ◽  
Support Vector ◽  
Svm Classifier ◽  
Good Prediction ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
High Throughput Experiments

In post-genomic biology, researchers in the field of proteome focus their attention on the networks of protein interactions that control the lives of cells and organisms. Protein-protein interactions play a useful role in dynamic cellular machinery. In this paper, we developed a method to infer protein-protein interactions based on the theory of support vector machine (SVM). For a given pair of proteins, a new strategy of calculating cross-correlation function of mRNA expression profiles was used to encode SVM vectors. We compared the performance with other methods of inferring protein-protein interaction. Results suggested that, through five-fold cross validation, our SVM model achieved a good prediction. It enables us to show that expression profiles in transcription level can be used to distinguish physical or functional interactions of proteins as well as sequence contents. Lastly, we applied our SVM classifier to evaluate data quality of interaction data sets from four high-throughput experiments. The results show that high-throughput experiments sacrifice some accuracy in determination of interactions because of limitation of experiment technologies.

scholarly journals Contacts-based prediction of binding affinity in protein–protein complexes

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Anna Vangone ◽  
Alexandre MJJ Bonvin
Keyword(s):  
Binding Affinity ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Prediction Accuracy ◽  
Protein Complexes ◽  
Structural Features ◽  
Specific Protein ◽  
Strong Impact ◽  
Protein Protein Interactions ◽  
Almost All

Almost all critical functions in cells rely on specific protein–protein interactions. Understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack a thorough understanding of the energetics of association of proteins. Here, we introduce a new and simple approach to predict binding affinity based on functional and structural features of the biological system, namely the network of interfacial contacts. We assess its performance against a protein–protein binding affinity benchmark and show that both experimental methods used for affinity measurements and conformational changes have a strong impact on prediction accuracy. Using a subset of complexes with reliable experimental binding affinities and combining our contacts and contact-types-based model with recent observations on the role of the non-interacting surface in protein–protein interactions, we reach a high prediction accuracy for such a diverse dataset outperforming all other tested methods.

scholarly journals An Efficient Feature Extraction Technique Based on Local Coding PSSM and Multifeatures Fusion for Predicting Protein-Protein Interactions

2019 ◽  
Vol 15 ◽  
pp. 117693431987992 ◽  
Author(s):  
Ji-Yong An ◽  
Yong Zhou ◽  
Yu-Jun Zhao ◽  
Zi-Ji Yan
Keyword(s):  
Feature Extraction ◽  
Protein Interactions ◽  
Functional Organization ◽  
Extraction Methods ◽  
Amino Acid Sequences ◽  
Evolutionary Information ◽  
Support Vector ◽  
Svm Classifier ◽  
Protein Protein Interactions ◽  
Local Coding

Background: Increasing evidence has indicated that protein-protein interactions (PPIs) play important roles in various aspects of the structural and functional organization of a cell. Thus, continuing to uncover potential PPIs is an important topic in the biomedical domain. Although various feature extraction methods with machine learning approaches have enhanced the prediction of PPIs. There remains room for improvement by developing novel and effective feature extraction methods and classifier approaches to identify PPIs. Method: In this study, we proposed a sequence-based feature extraction method called LCPSSMMF, which combined local coding position-specific scoring matrix (PSSM) with multifeatures fusion. First, we used a novel local coding method based on PSSM to build a new PSSM (CPSSM); the advantage of this method is that it incorporated global and local feature extraction, which can account for the interactions between residues in both continuous and discontinuous regions of amino acid sequences. Second, we adopted 2 different feature extraction methods (Local Average Group [LAG] and Bigram Probability [BP]) to capture multiple key feature information by employing the evolutionary information embedded in the CPSSM matrix. Finally, feature vectors were acquired by using multifeatures fusion method. Result: To evaluate the performance of the proposed feature extraction approach, we employed support vector machine (SVM) as a prediction classifier and applied this method to yeast and human PPI datasets. The prediction accuracies of LCPSSMMF were 93.43% and 90.41% on the yeast and human datasets, respectively. Moreover, we also compared the proposed method with the previous sequence-based approaches on the yeast datasets by using the same SVM classifier. The experimental results indicated that the performance of LCPSSMMF significantly exceeded that of several other state-of-the-art methods. It is proven that the LCPSSMMF approach can capture more local and global discriminatory information than almost all previous methods and can function remarkably well in identifying PPIs. To facilitate extensive research in future proteomics studies, we developed a LCPSSMMFSVM server, which is freely available for academic use at http://219.219.62.123:8888/LCPSSMMFSVM .

scholarly journals 2P2I HUNTER : a tool for filtering orthosteric protein–protein interaction modulators via a dedicated support vector machine

2014 ◽  
Vol 11 (90) ◽  
pp. 20130860 ◽  
Author(s):  
Véronique Hamon ◽  
Raphael Bourgeas ◽  
Pierre Ducrot ◽  
Isabelle Theret ◽  
Laura Xuereb ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Protein Interactions ◽  
High Throughput Screening ◽  
Chemical Space ◽  
Support Vector ◽  
Protein Protein Interactions ◽  
Target Class ◽  
Chemical Library ◽  
Protein Protein Interaction ◽  
Svm Model

Over the last 10 years, protein–protein interactions (PPIs) have shown increasing potential as new therapeutic targets. As a consequence, PPIs are today the most screened target class in high-throughput screening (HTS). The development of broad chemical libraries dedicated to these particular targets is essential; however, the chemical space associated with this ‘high-hanging fruit’ is still under debate. Here, we analyse the properties of 40 non-redundant small molecules present in the 2P2I database ( http://2p2idb.cnrs-mrs.fr/ ) to define a general profile of orthosteric inhibitors and propose an original protocol to filter general screening libraries using a support vector machine (SVM) with 11 standard D ragon molecular descriptors. The filtering protocol has been validated using external datasets from PubChem BioAssay and results from in-house screening campaigns . This external blind validation demonstrated the ability of the SVM model to reduce the size of the filtered chemical library by eliminating up to 96% of the compounds as well as enhancing the proportion of active compounds by up to a factor of 8. We believe that the resulting chemical space identified in this paper will provide the scientific community with a concrete support to search for PPI inhibitors during HTS campaigns.

scholarly journals Using Weighted Sparse Representation Model Combined with Discrete Cosine Transformation to Predict Protein-Protein Interactions from Protein Sequence

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yu-An Huang ◽  
Zhu-Hong You ◽  
Xin Gao ◽  
Leon Wong ◽  
Lirong Wang
Keyword(s):  
Sparse Representation ◽  
Protein Interactions ◽  
Protein Sequence ◽  
False Positive Rate ◽  
Computational Method ◽  
Substitution Matrix ◽  
Support Vector ◽  
Svm Classifier ◽  
Protein Protein Interactions ◽  
Discrete Cosine Transformation

Increasing demand for the knowledge about protein-protein interactions (PPIs) is promoting the development of methods for predicting protein interaction network. Although high-throughput technologies have generated considerable PPIs data for various organisms, it has inevitable drawbacks such as high cost, time consumption, and inherently high false positive rate. For this reason, computational methods are drawing more and more attention for predicting PPIs. In this study, we report a computational method for predicting PPIs using the information of protein sequences. The main improvements come from adopting a novel protein sequence representation by using discrete cosine transform (DCT) on substitution matrix representation (SMR) and from using weighted sparse representation based classifier (WSRC). When performing on the PPIs dataset ofYeast,Human, andH. pylori, we got excellent results with average accuracies as high as 96.28%, 96.30%, and 86.74%, respectively, significantly better than previous methods. Promising results obtained have proven that the proposed method is feasible, robust, and powerful. To further evaluate the proposed method, we compared it with the state-of-the-art support vector machine (SVM) classifier. Extensive experiments were also performed in which we usedYeastPPIs samples as training set to predict PPIs of other five species datasets.

scholarly journals Computational Prediction of Protein-Protein Interactions in Plants Using Only Sequence Information

2021 ◽  
Author(s):  
Jie. Pan ◽  
Zhu Hong. You ◽  
Li Ping. Li ◽  
Chang-Qing. Yu ◽  
Xin-Ke. Zhan
Keyword(s):  
Plant Cell ◽  
Protein Interactions ◽  
Cell Function ◽  
Functional Organization ◽  
Computational Prediction ◽  
Support Vector ◽  
Svm Classifier ◽  
Sequence Information ◽  
Protein Protein Interactions ◽  
Representation Scheme

Abstract Protein-protein interactions (PPIs) in plants plays a significant role in plant biology and functional organization of cells. Although, a large amount of plant PPIs data have been generated by high-throughput techniques, but due to the complexity of plant cell, the PPIs pairs currently obtained by experimental methods cover only a small fraction of the complete plant PPIs network. In addition, the experimental approaches for identifying PPIs in plants are laborious, time-consuming, and costly. Hence, it is highly desirable to develop more efficient approaches to detect PPIs in plants. In this study, we present a novel computational model combining weighted sparse representation-based classifier (WSRC) with a novel inverse fast Fourier transform (IFFT) representation scheme which was adopted in position specific scoring matrix (PSSM) to extract features from plant protein sequence. When performed the proposed method on the plants PPIs dataset of Mazie, Rice and Arabidopsis thaliana (Arabidopsis), we achieved excellent results with high accuracies of 89.12%, 84.72% and 71.74%, respectively. To further assess the prediction performance of the proposed approach, we compared it with the state-of-art support vector machine (SVM) classifier. To the best of our knowledge, we are the first to employ protein sequences information to predict PPIs in plants. Experimental results demonstrate that the proposed method has a great potential to become a powerful tool for exploring the plant cell function.

Prediction of Disease Comorbidity Using HeteSim Scores based on Multiple Heterogeneous Networks

2019 ◽  
Vol 19 (4) ◽  
pp. 232-241 ◽  
Author(s):  
Xuegong Chen ◽  
Wanwan Shi ◽  
Lei Deng
Keyword(s):  
Protein Interactions ◽  
Experimental Studies ◽  
Treatment Strategies ◽  
Computational Method ◽  
Biological Information ◽  
Support Vector ◽  
Protein Protein Interactions ◽  
Efficient Treatment ◽  
Disease Associations ◽  
Previous State

Background: Accumulating experimental studies have indicated that disease comorbidity causes additional pain to patients and leads to the failure of standard treatments compared to patients who have a single disease. Therefore, accurate prediction of potential comorbidity is essential to design more efficient treatment strategies. However, only a few disease comorbidities have been discovered in the clinic. Objective: In this work, we propose PCHS, an effective computational method for predicting disease comorbidity. Materials and Methods: We utilized the HeteSim measure to calculate the relatedness score for different disease pairs in the global heterogeneous network, which integrates six networks based on biological information, including disease-disease associations, drug-drug interactions, protein-protein interactions and associations among them. We built the prediction model using the Support Vector Machine (SVM) based on the HeteSim scores. Results and Conclusion: The results showed that PCHS performed significantly better than previous state-of-the-art approaches and achieved an AUC score of 0.90 in 10-fold cross-validation. Furthermore, some of our predictions have been verified in literatures, indicating the effectiveness of our method.

scholarly journals ALPINE: Active Link Prediction Using Network Embedding

2021 ◽  
Vol 11 (11) ◽  
pp. 5043
Author(s):  
Xi Chen ◽  
Bo Kang ◽  
Jefrey Lijffijt ◽  
Tijl De Bie
Keyword(s):  
Active Learning ◽  
Protein Interactions ◽  
Link Prediction ◽  
Prediction Accuracy ◽  
Real Data ◽  
Network Embedding ◽  
Protein Protein Interactions ◽  
Additional Information ◽  
The Cost ◽  
Active Link

Many real-world problems can be formalized as predicting links in a partially observed network. Examples include Facebook friendship suggestions, the prediction of protein–protein interactions, and the identification of hidden relationships in a crime network. Several link prediction algorithms, notably those recently introduced using network embedding, are capable of doing this by just relying on the observed part of the network. Often, whether two nodes are linked can be queried, albeit at a substantial cost (e.g., by questionnaires, wet lab experiments, or undercover work). Such additional information can improve the link prediction accuracy, but owing to the cost, the queries must be made with due consideration. Thus, we argue that an active learning approach is of great potential interest and developed ALPINE (Active Link Prediction usIng Network Embedding), a framework that identifies the most useful link status by estimating the improvement in link prediction accuracy to be gained by querying it. We proposed several query strategies for use in combination with ALPINE, inspired by the optimal experimental design and active learning literature. Experimental results on real data not only showed that ALPINE was scalable and boosted link prediction accuracy with far fewer queries, but also shed light on the relative merits of the strategies, providing actionable guidance for practitioners.

scholarly journals Identification of the Disrupted Pathways Associated with Periodontitis Based on Human Pathway Network

2016 ◽  
Vol 5 (4) ◽  
pp. 93-98
Author(s):  
Wen Sun ◽  
Lin Han ◽  
Wenmao Xu ◽  
Yazhen Sun
Keyword(s):  
Protein Interactions ◽  
Threshold Value ◽  
Normal Subjects ◽  
Protein Protein Interactions ◽  
Pathway Network ◽  
Differential Expression Genes ◽  
Weight Value ◽  
Limma Package ◽  
Novel Method ◽  
Cognitively Normal Subjects

AbstractObjective: The objective of this work is to search for a novel method to explore the disrupted pathways associated with periodontitis (PD) based on the network level.Methods: Firstly, the differential expression genes (DEGs) between PD patients and cognitively normal subjects were inferred based on LIMMA package. Then, the protein-protein interactions (PPI) in each pathway were explored by Empirical Bayesian (EB) co-expression program. Specifically, we determined the 100th weight value as the threshold value of the disrupted pathways of PPI by constructing the randomly model and confirmed the weight value of each pathway. Meanwhile, we dissected the disrupted pathways under the weight value > the threshold value. Pathways enrichment analyses of DEGs were carried out based on Expression Analysis Systematic Explored (EASE) test. Finally, the better method was selected based on the more rich and significant obtained pathways by comparing the two methods.Results: After the calculation of LIMMA package, we estimated 524 DEGs in all. Then we determined 0.115222 as the threshold value of the disrupted pathways of PPI. When the weight value>0.115222, there were 258 disrupted pathways of PPI enriched in. Additionally, we observed those 524 DEGs that were enriched in 4 pathways under EASE=0.1.Conclusion: We proposed a novel network method inferring the disrupted pathway for PD. The disrupted pathways might be underlying biomarkers for treatment associated with PD.

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