NDLI: Prediction of Protein–Protein Interactions with Clustered Amino Acids and Weighted Sparse Representation

Content Provider	PubMed Central
Author	Huang, Qiaoying You, Zhuhong Zhang, Xiaofeng Zhou, Yong
Editor	Karabencheva-christova, Tatyana
Copyright Year	2015
Abstract	With the completion of the Human Genome Project, bioscience has entered into the era of the genome and proteome. Therefore, protein–protein interactions (PPIs) research is becoming more and more important. Life activities and the protein–protein interactions are inseparable, such as DNA synthesis, gene transcription activation, protein translation, etc. Though many methods based on biological experiments and machine learning have been proposed, they all spent a long time to learn and obtained an imprecise accuracy. How to efficiently and accurately predict PPIs is still a big challenge. To take up such a challenge, we developed a new predictor by incorporating the reduced amino acid alphabet (RAAA) information into the general form of pseudo-amino acid composition (PseAAC) and with the weighted sparse representation-based classification (WSRC). The remarkable advantages of introducing the reduced amino acid alphabet is being able to avoid the notorious dimensionality disaster or overfitting problem in statistical prediction. Additionally, experiments have proven that our method achieved good performance in both a low- and high-dimensional feature space. Among all of the experiments performed on the PPIs data of Saccharomyces cerevisiae, the best one achieved 90.91% accuracy, 94.17% sensitivity, 87.22% precision and a 83.43% Matthews correlation coefficient (MCC) value. In order to evaluate the prediction ability of our method, extensive experiments are performed to compare with the state-of-the-art technique, support vector machine (SVM). The achieved results show that the proposed approach is very promising for predicting PPIs, and it can be a helpful supplement for PPIs prediction.
Related Links	http://dx.doi.org/10.3390/ijms160510855
Ending Page	10869
Page Count	15
Starting Page	10855
File Format	PDF
ISSN	14220067
e-ISSN	14220067
Journal	International Journal of Molecular Sciences
Issue Number	5
Volume Number	16
Language	English
Publisher	MDPI
Publisher Date	2015-05-13
Access Restriction	Open
Rights Holder	MDPI
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Organic Chemistry Medicine Molecular Biology Physical and Theoretical Chemistry Catalysis Inorganic Chemistry Computer Science Applications

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Prediction of Protein–Protein Interactions with Clustered Amino Acids and Weighted Sparse Representation

Reconstructing a Flavodoxin Oxidoreductase with Early Amino Acids

Supernovae, Neutrinos and the Chirality of Amino Acids

Prediction of Protein–Protein Interaction with Pairwise Kernel Support Vector Machine

Protein Dynamics: From Molecules, to Interactions, to Biology

Structure Prediction of Partial-Length Protein Sequences

Three-Dimensional Structural Aspects of Protein–Polysaccharide Interactions

Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods

Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition

Prediction of Protein–Protein Interactions with Clustered Amino Acids and Weighted Sparse Representation

Similar Documents

Prediction of Protein–Protein Interactions with Clustered Amino Acids and Weighted Sparse Representation

Reconstructing a Flavodoxin Oxidoreductase with Early Amino Acids

Supernovae, Neutrinos and the Chirality of Amino Acids

Prediction of Protein–Protein Interaction with Pairwise Kernel Support Vector Machine

Protein Dynamics: From Molecules, to Interactions, to Biology

Structure Prediction of Partial-Length Protein Sequences

Three-Dimensional Structural Aspects of Protein–Polysaccharide Interactions

Recent Progress in Treating Protein–Ligand Interactions with Quantum-Mechanical Methods

Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition

Prediction of Protein–Protein Interactions with Clustered Amino Acids and Weighted Sparse Representation