Literature DB >> 27866233

A Treatise to Computational Approaches Towards Prediction of Membrane Protein and Its Subtypes.

Ahmad Hassan Butt1, Nouman Rasool2, Yaser Daanial Khan3.   

Abstract

Membrane proteins are vital mediating molecules responsible for the interaction of a cell with its surroundings. These proteins are involved in different functionalities such as ferrying of molecules and nutrients across membrane, recognizing foreign bodies, receiving outside signals and translating them into the cell. Membrane proteins play significant role in drug interaction as nearly 50% of the drug targets are membrane proteins. Due to the momentous role of membrane protein in cell activity, computational models able to predict membrane protein with accurate measures bears indispensable importance. The conventional experimental methods used for annotating membrane proteins are time-consuming and costly and in some cases impossible. Computationally intelligent techniques have emerged to be as a useful resource in the automation of prediction and hence the annotation process. In this study, various techniques have been reviewed that are based on different computational intelligence models used for prediction process. These techniques were formulated by different researchers and were further evaluated to provide a comparative analysis. Analysis shows that the usage of support vector machine-based prediction techniques bears more assiduous results.

Keywords:  Amino acids; Membrane proteins; Position-specific scoring matrix; Probabilistic neural networks; Pseudo amino acids compositions; Support vector machine

Mesh:

Substances:

Year:  2016        PMID: 27866233     DOI: 10.1007/s00232-016-9937-7

Source DB:  PubMed          Journal:  J Membr Biol        ISSN: 0022-2631            Impact factor:   1.843


  58 in total

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Journal:  Adv Protein Chem       Date:  1954

2.  Using GO-PseAA predictor to predict enzyme sub-class.

Authors:  Kuo-Chen Chou; Yu-Dong Cai
Journal:  Biochem Biophys Res Commun       Date:  2004-12-10       Impact factor: 3.575

3.  Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method.

Authors:  Jaehyun Sim; Seung-Yeon Kim; Julian Lee
Journal:  Bioinformatics       Date:  2005-04-06       Impact factor: 6.937

4.  Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition.

Authors:  Hong-Bin Shen; Jie Yang; Kuo-Chen Chou
Journal:  J Theor Biol       Date:  2005-09-28       Impact factor: 2.691

5.  Using GO-PseAA predictor to identify membrane proteins and their types.

Authors:  Kuo-Chen Chou; Yu-Dong Cai
Journal:  Biochem Biophys Res Commun       Date:  2005-02-18       Impact factor: 3.575

6.  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

7.  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

8.  SLLE for predicting membrane protein types.

Authors:  Meng Wang; Jie Yang; Zhi-Jie Xu; Kuo-Chen Chou
Journal:  J Theor Biol       Date:  2005-01-07       Impact factor: 2.691

9.  The fluid mosaic model of the structure of cell membranes.

Authors:  S J Singer; G L Nicolson
Journal:  Science       Date:  1972-02-18       Impact factor: 47.728

10.  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

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  15 in total

1.  Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.

Authors:  Giray Enkavi; Matti Javanainen; Waldemar Kulig; Tomasz Róg; Ilpo Vattulainen
Journal:  Chem Rev       Date:  2019-03-12       Impact factor: 60.622

2.  iPhosY-PseAAC: identify phosphotyrosine sites by incorporating sequence statistical moments into PseAAC.

Authors:  Yaser Daanial Khan; Nouman Rasool; Waqar Hussain; Sher Afzal Khan; Kuo-Chen Chou
Journal:  Mol Biol Rep       Date:  2018-10-11       Impact factor: 2.316

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

Authors:  Ahmad Hassan Butt; Nouman Rasool; Yaser Daanial Khan
Journal:  Mol Biol Rep       Date:  2018-09-20       Impact factor: 2.316

4.  TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information.

Authors:  Munira Alballa; Faizah Aplop; Gregory Butler
Journal:  PLoS One       Date:  2020-01-14       Impact factor: 3.240

5.  Detection of Weakly Expressed Trypanosoma cruzi Membrane Proteins Using High-Performance Probes.

Authors:  Teresa Cruz-Bustos; Silvia N J Moreno; Roberto Docampo
Journal:  J Eukaryot Microbiol       Date:  2018-03-30       Impact factor: 3.346

6.  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

7.  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

8.  iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou's 5-steps Rule and Pseudo Components.

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

9.  A Novel Modeling in Mathematical Biology for Classification of Signal Peptides.

Authors:  Asma Ehsan; Khalid Mahmood; Yaser Daanial Khan; Sher Afzal Khan; Kuo-Chen Chou
Journal:  Sci Rep       Date:  2018-01-18       Impact factor: 4.379

10.  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

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