Literature DB >> 30238411

Predicting membrane proteins and their types by extracting various sequence features into Chou's general PseAAC.

Ahmad Hassan Butt1, Nouman Rasool2, Yaser Daanial Khan3.   

Abstract

For many biological functions membrane proteins (MPs) are considered crucial. Due to this nature of MPs, many pharmaceutical agents have reflected them as attractive targets. It bears indispensable importance that MPs are predicted with accurate measures using effective and efficient computational models (CMs). Annotation of MPs using in vitro analytical techniques is time-consuming and expensive; and in some cases, it can prove to be intractable. Due to this scenario, automated prediction and annotation of MPs through CM based techniques have appeared to be useful. Based on the use of computational intelligence and statistical moments based feature set, an MP prediction framework is proposed. Furthermore, the previously used dataset has been enhanced by incorporating new MPs from the latest release of UniProtKB. Rigorous experimentation proves that the use of statistical moments with a multilayer neural network, trained using back-propagation based prediction techniques allows more thorough results.

Keywords:  Amino acids; Confusion matrix; Jackknife tests; Mathew’s correlation coefficient; Membrane proteins; Neural networks

Mesh:

Substances:

Year:  2018        PMID: 30238411     DOI: 10.1007/s11033-018-4391-5

Source DB:  PubMed          Journal:  Mol Biol Rep        ISSN: 0301-4851            Impact factor:   2.316


  83 in total

1.  Relation between amino acid composition and cellular location of proteins.

Authors:  J Cedano; P Aloy; J A Pérez-Pons; E Querol
Journal:  J Mol Biol       Date:  1997-02-28       Impact factor: 5.469

2.  pLoc_bal-mGpos: Predict subcellular localization of Gram-positive bacterial proteins by quasi-balancing training dataset and PseAAC.

Authors:  Xuan Xiao; Xiang Cheng; Genqiang Chen; Qi Mao; Kuo-Chen Chou
Journal:  Genomics       Date:  2018-05-26       Impact factor: 5.736

3.  pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC.

Authors:  Xiang Cheng; Xuan Xiao; Kuo-Chen Chou
Journal:  Genomics       Date:  2017-08-14       Impact factor: 5.736

4.  iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory.

Authors:  Wang-Ren Qiu; Bi-Qian Sun; Xuan Xiao; Dong Xu; Kuo-Chen Chou
Journal:  Mol Inform       Date:  2016-05-12       Impact factor: 3.353

5.  A multilabel model based on Chou's pseudo-amino acid composition for identifying membrane proteins with both single and multiple functional types.

Authors:  Chao Huang; Jing-Qi Yuan
Journal:  J Membr Biol       Date:  2013-04-02       Impact factor: 1.843

6.  Using Chou's general PseAAC to analyze the evolutionary relationship of receptor associated proteins (RAP) with various folding patterns of protein domains.

Authors:  S Muthu Krishnan
Journal:  J Theor Biol       Date:  2018-02-22       Impact factor: 2.691

7.  Prediction of N-linked glycosylation sites using position relative features and statistical moments.

Authors:  Muhammad Aizaz Akmal; Nouman Rasool; Yaser Daanial Khan
Journal:  PLoS One       Date:  2017-08-10       Impact factor: 3.240

8.  iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences.

Authors:  Wei Chen; Pengmian Feng; Hui Yang; Hui Ding; Hao Lin; Kuo-Chen Chou
Journal:  Oncotarget       Date:  2017-01-17

9.  Some remarks on protein attribute prediction and pseudo amino acid composition.

Authors:  Kuo-Chen Chou
Journal:  J Theor Biol       Date:  2010-12-17       Impact factor: 2.691

10.  iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition.

Authors:  Wei Chen; Peng-Mian Feng; Hao Lin; Kuo-Chen Chou
Journal:  Biomed Res Int       Date:  2014-05-21       Impact factor: 3.411

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Journal:  Mol Genet Genomics       Date:  2020-01-01       Impact factor: 3.291

2.  iMethylK_pseAAC: Improving Accuracy of Lysine Methylation Sites Identification by Incorporating Statistical Moments and Position Relative Features into General PseAAC via Chou's 5-steps Rule.

Authors:  Sarah Ilyas; Waqar Hussain; Adeel Ashraf; Yaser Daanial Khan; Sher Afzal Khan; Kuo-Chen Chou
Journal:  Curr Genomics       Date:  2019-05       Impact factor: 2.236

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Authors:  Omar Barukab; Yaser Daanial Khan; Sher Afzal Khan; Kuo-Chen Chou
Journal:  Curr Genomics       Date:  2019-05       Impact factor: 2.236

4.  A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns.

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5.  Evaluating machine learning methodologies for identification of cancer driver genes.

Authors:  Sharaf J Malebary; Yaser Daanial Khan
Journal:  Sci Rep       Date:  2021-06-10       Impact factor: 4.379

6.  iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule.

Authors:  Sharaf Jameel Malebary; Muhammad Safi Ur Rehman; Yaser Daanial Khan
Journal:  PLoS One       Date:  2019-11-21       Impact factor: 3.240

7.  TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings.

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Journal:  BMC Med Genomics       Date:  2020-10-22       Impact factor: 3.063

8.  iAcety-SmRF: Identification of Acetylation Protein by Using Statistical Moments and Random Forest.

Authors:  Sharaf Malebary; Shaista Rahman; Omar Barukab; Rehab Ash'ari; Sher Afzal Khan
Journal:  Membranes (Basel)       Date:  2022-02-25
  8 in total

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