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Human Protein Subcellular Localization with Integrated Source and Multi-label Ensemble Classifier

Xiaotong Guo, Fulin Liu, Ying Ju, Zhen Wang, Chunyu Wang
2016 Scientific Reports  
However, none of the current works on computational protein subcellular localization have integrated these sources. Only part of the protein sequences were employed for training in previous works.  ...  , (3) design of multi-label classification algorithm, and (4) construction of Web server 6 .  ...  F.L.L. helped to collect the protein localization data. Y.J. helped to revise the English. Z.W. participated in the design of the experiments.  ... 
doi:10.1038/srep28087 pmid:27323846 pmcid:PMC4914962 fatcat:6whwbxlrmnd53npijlaft7zohy

Multi-Site Protein Subcellular Localization Based on Deep Convolutional Neural Network

Hanhan Cong, Hong Liu, Yuehui Chen, Yaou Zhao, Lei Wang
2019 Journal of Nutritional Biology  
This paper proposed an algorithm based deep convolution neural network which is suit for multi-site protein subcellular localization and the algorithm is implemented on the human protein database to verify  ...  It can be inferred from experiments that the proposed algorithm is effective in multi-site protein subcellular localization and the overall correct rate of classification is 59.13% which is higher than  ...  The classification results were compared with MLKNN and ICNN which achieved good results in multi-site protein subcellular localization on the dataset.  ... 
doi:10.18314/jnb.v5i1.1580 fatcat:ice4fvofsjh6vgxmowxd4vgik4

Protein Subcellular Localization Based on Evolutionary Information and Segmented Distribution

Danyu Jin, Ping Zhu, Nianyin Zeng
2021 Mathematical Problems in Engineering  
The prediction of protein subcellular localization not only is important for the study of protein structure and function but also can facilitate the design and development of new drugs.  ...  In order to reflect the protein sequence information as much as possible, AAO method, PSSM-AAO method, and PSSM-GSD method are fused together.  ...  For the classification prediction model of protein subcellular localization, the traditional algorithms mainly include support vector machine (SVM) [14, 15] , K-nearest neighbor algorithm (KNN) [16]  ... 
doi:10.1155/2021/8629776 fatcat:nki7mgzjvjdsvjh3azsatofdxa

A Dynamic-time Distance Based on Wavelet Decomposition for Subcellular Localization Classification

Cuifang Gao, Wanqiang Shen, Yanglijun Zhang
2020 IEEE Access  
to achieve the subcellular localization prediction for unknown proteins in the future.  ...  In the present study, according to the characteristics of protein sequences, a novel algorithm for the identification of the subcellular protein localization based on Wavelet Packet Decomposition and Dynamic  ... 
doi:10.1109/access.2020.3040555 fatcat:af2hmpvn3vfdvkidvyh4eobr2a

pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties

Deepak Sarda, Gek Huey Chua, Kuo-Bin Li, Arun Krishnan
2005 BMC Bioinformatics  
Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed.  ...  Unlike other algorithms, contextual information is preserved by dividing the protein sequences into clusters.  ...  Acknowledgements The authors would like to acknowledge Tariq Riaz and Jiren Wang for their inputs during several helpful discussions.  ... 
doi:10.1186/1471-2105-6-152 pmid:15963230 pmcid:PMC1182350 fatcat:ep2ls55z35gxvldatx7lofupa4

Prediction Methods of the Protein Subcellular Localization: A Systematic Reviews

Arli Aditya Parikesit, Gabriella Patricia, Nanda Risqia Pradana Ratnasari
2019 Indonesian Journal of Life Sciences  
The prediction of protein subcellular localization (SCL) has been a long-running challenge in bioinformatics. Protein SCL is crucial for a protein to exercise its functions properly.  ...  SCL methods can be classified as either sequence-based or annotation-based. Machine learning algorithms and classifiers are used in protein SCL prediction tools.  ...  ACKNOWLEDGEMENTS The authors would like to thanks Institute for Research and Corporate Social Responsibility of Indonesia International Institute for Life Sciences for supporting the development of this  ... 
doi:10.54250/ijls.v1i2.20 fatcat:tdxhdc62xfhqdhm22qjnbmjrxu

Accurate prediction of subcellular location of apoptosis proteins combining Chou's PseAAC and PsePSSM based on wavelet denoising

Bin Yu, Shan Li, Wen-Ying Qiu, Cheng Chen, Rui-Xin Chen, Lei Wang, Ming-Hui Wang, Yan Zhang
2017 OncoTarget  
In this paper, we propose a novel method for protein subcellular localization prediction.  ...  Apoptosis proteins subcellular localization information are very important for understanding the mechanism of programmed cell death and the development of drugs.  ...  ACKNOWLEDGMENTS The authors would like to thank all anonymous reviewers for their constructive comments that have improved this manuscript.  ... 
doi:10.18632/oncotarget.22585 pmid:29296195 pmcid:PMC5746097 fatcat:uzbtwp5fivbnxl3ycqqgua7o34

Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains

Alla Bulashevska, Roland Eils
2006 BMC Bioinformatics  
This study introduces an algorithm which uses only the primary sequence of a protein to predict its subcellular location.  ...  It would be worthwhile to develop a method to predict the subcellular location for a given protein when only the amino acid sequence of the protein is known.  ...  This can result in missing or only partially included leader sequences, thereby causing problems for sequence-motifbased localization algorithms.  ... 
doi:10.1186/1471-2105-7-298 pmid:16774677 pmcid:PMC1525000 fatcat:nf2nkd5g5vcq5dnfx5j6v2fsrq

Prediction of Apoptosis Protein Subcellular Localization with Multilayer Sparse Coding and Oversampling Approach

Xingjian Chen, Xuejiao Hu, Wenxin Yi, Xiang Zou, Wei Xue
2019 BioMed Research International  
In order to improve the prediction accuracy of apoptosis protein subcellular localization, we proposed a sparse coding method combined with traditional feature extraction algorithm to complete the sparse  ...  The prediction of apoptosis protein subcellular localization plays an important role in understanding the progress in cell proliferation and death.  ...  Acknowledgments This work was partially supported by National Key R&D Program of China (2017YFD0800204) and the Fundamental Research Funds for the Central Universities (No. KYZ201600175).  ... 
doi:10.1155/2019/2436924 fatcat:oarherjbfrb3jl57hbbypaorpa

Multisite protein subcellular localization prediction based on entropy density

Qing Zhao, Dong Wang, Yuehui Chen, Xumi Qu, Feng Liu, Dong-Hoon Lee, Ricardo Lagoa, Sandeep Kumar
2015 Bio-medical materials and engineering  
Protein subcellular localization prediction is currently receiving much attention in the field of protein research.  ...  Many researchers make great efforts to study single-site protein subcellular localization, but the experimental data shows that many proteins can be found in two or more sub-cellular locations, prompting  ...  Predicting protein subcellular localization has been a hot topic for many years, and researchers have made great efforts to predict protein subcellular localization and established numerous effective prediction  ... 
doi:10.3233/bme-151504 pmid:26405976 fatcat:r2l6zg7vmfbhbdxsecg5za6gfy

Esub8: a novel tool to predict protein subcellular localizations in eukaryotic organisms

Qinghua Cui, Tianzi Jiang, Bing Liu, Songde Ma
2004 BMC Bioinformatics  
Subcellular localization of a new protein sequence is very important and fruitful for understanding its function.  ...  Our method is tested in three subcellular localization predictions for prokaryotic proteins and four subcellular localization predictions for eukaryotic proteins on Reinhardt's dataset.  ...  Budy for some language corrections.  ... 
doi:10.1186/1471-2105-5-66 pmid:15163352 pmcid:PMC420457 fatcat:eovoraji45eytjlmv66lhkctaq

Support vector machine approach for protein subcellular localization prediction

S. Hua, Z. Sun
2001 Bioinformatics  
A fully automatic and reliable prediction system for protein subcellular localization is needed, especially for the analysis of large-scale genome sequences.  ...  Motivation: Subcellular localization is a key functional characteristic of proteins.  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr A.Reinhardt (Wellcome Trust Genome Campus, Hinxton, UK) for providing the dataset.  ... 
doi:10.1093/bioinformatics/17.8.721 pmid:11524373 fatcat:bnvkqa7sdzf3hgz47lqi3yeb5u

An Ensemble Classifier for Eukaryotic Protein Subcellular Location Prediction Using Gene Ontology Categories and Amino Acid Hydrophobicity

Liqi Li, Yuan Zhang, Lingyun Zou, Changqing Li, Bo Yu, Xiaoqi Zheng, Yue Zhou, Vladimir Brusic
2012 PLoS ONE  
With the rapid increase of protein sequences in the post-genomic age, it is challenging to develop accurate and automated methods for reliably and quickly predicting their subcellular localizations.  ...  In this paper, we proposed an ensemble classifier of KNN (k-nearest neighbor) and SVM (support vector machine) algorithms to predict the subcellular localization of eukaryotic proteins based on a voting  ...  Acknowledgments The authors thank Ning Huang and Yan Yu whose constructive comments are very helpful for strengthening the presentation of this paper. Author Contributions  ... 
doi:10.1371/journal.pone.0031057 pmid:22303481 pmcid:PMC3268814 fatcat:4az4d23acjhelfooqxlwyiasga

Fast Fourier Transform-based Support Vector Machine for Subcellular Localization Prediction Using Different Substitution Models

Zhimeng WANG, Lin JIANG, Menglong LI, Lina SUN, Rongying LIN
2007 Acta Biochimica et Biophysica Sinica  
There are approximately 10 9 proteins in a cell. A hotspot in bioinformatics is how to identify a protein's subcellular localization, if its sequence is known.  ...  In this paper, a method using fast Fourier transform-based support vector machine is developed to predict the subcellular localization of proteins from their physicochemical properties and structural parameters  ...  But higher predictive accuracy is still an aim for these algorithms. In this paper, a new method for predicting protein subcellular localization is introduced.  ... 
doi:10.1111/j.1745-7270.2007.00326.x pmid:17805467 fatcat:ibp3g5lbwbbl7joek6s4ctjvsy

Predicting Protein Subcellular Localization Using the Algorithm of Diversity Finite Coefficient Combined with Artificial Neural Network

Ze Yue Wu, Yue Hui Chen
2013 Advanced Materials Research  
The subcellular localization of proteins classification problem is transformed into several two classification problems with error-correcting output codes.  ...  Protein subcellular localization is an important research field of bioinformatics.  ...  Various approaches for protein subcellular localization prediction have been developed according to protein sequence information.  ... 
doi:10.4028/www.scientific.net/amr.756-759.3760 fatcat:cnfcnouxdvczrk6dtyqi4wglrq
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