Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences

Liu, Bin; Wu, Hao; Chou, Kuo‐Chen

doi:10.4236/ns.2017.94007

Cited by 127 publications

(96 citation statements)

References 223 publications

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“…Ever since the concept of Chou's PseAAC was proposed, it has been widely used in nearly all the areas of computational proteomics as well as a long list of references . Therefore, incorporating the results from the current study into Chou's PseAAC could facilitate for a better ubi prediction tool. As pointed out by Shen, user‐friendly and publicly accessible web‐servers represent the future direction.…”

Section: Discussionmentioning

confidence: 97%

Sequence and structure‐based characterization of ubiquitination sites in human and yeast proteins using Chou's sample formulation

Kumar

Vellaichamy

2019

Proteins

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Ubiquitination is an important post‐translational event responsible for half‐life and turnover of proteins inside the cell. Proteins are ubiquitinated by forming an iso‐peptide bond between their lysine residue and C‐terminal glycine residue of ubiquitin leading to rapid degradation of proteins by 26S proteosome complex. Deregulation of ubiquitination is manifested by aberrant expression of E3‐ligase activity or mutation in the surroundings of ubiquitination sites. Many new experimentally validated ubiquitinated lysines have been recently identified that motivated the study of the environments surrounding the ubiquitinated lysines. With the help of known ubiquitinated proteins, here we present a comprehensive study of sequence and spatial environment of ubiquitination sites of human and yeast proteins. To identify position‐specific features, this work distinguishes the spatial environments as proximity and distal regions. Certain amino acids specific to these regions, well differentiate the ubiquitination sites from non‐ubiquitination sites are revealed. Additionally, amino acid signatures that contribute for protein disordered regions and solvent accessibility of amino acids are found to be contributing factors in ubiquitination sites. These results suggest that the ubiquitination site environment of the substrate determines the recognition and unfolding of substrate to facilitate the entry into 26S proteosomal complex. We believe that these findings will help in better prediction of ubiquitination sites using the sequence and spatial information.

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Section: Discussionmentioning

confidence: 97%

Sequence and structure‐based characterization of ubiquitination sites in human and yeast proteins using Chou's sample formulation

Kumar

Vellaichamy

2019

Proteins

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“…Encouraged by the success of using PseAAC to deal with protein/peptide sequences, the concept of PseKNC (pseudo K-tuple nucleotide composition) [79,80] was developed for generating various feature vectors for DNA/RNA sequences [81,82] that have proved useful as well [83][84][85][86][87][88][89][90]. Particularly, recently a powerful Web server called 'Pse-in-One' [91] and its updated version 'Psein-One2.0' [92] have been established that can be used to generate any desired feature vectors for protein/peptide and DNA/RNA sequences according to the need of users' studies.…”

Section: Sequence or Sequence-derived Featuresmentioning

confidence: 99%

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

Song

Wang

et al. 2018

Briefings in Bioinformatics

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160

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Regulation of proteolysis plays a critical role in a myriad of important cellular processes. The key to better understanding the mechanisms that control this process is to identify the specific substrates that each protease targets. To address this, we have developed iProt-Sub, a powerful bioinformatics tool for the accurate prediction of protease-specific substrates and their cleavage sites. Importantly, iProt-Sub represents a significantly advanced version of its successful predecessor, PROSPER. It provides optimized cleavage site prediction models with better prediction performance and coverage for more species-specific proteases (4 major protease families and 38 different proteases). iProt-Sub integrates heterogeneous sequence and structural features and uses a two-step feature selection procedure to further remove redundant and irrelevant features in an effort to improve the cleavage site prediction accuracy. Features used by iProt-Sub are encoded by 11 different sequence encoding schemes, including local amino acid sequence profile, secondary structure, solvent accessibility and native disorder, which will allow a more accurate representation of the protease specificity of approximately 38 proteases and training of the prediction models. Benchmarking experiments using cross-validation and independent tests showed that iProt-Sub is able to achieve a better performance than several existing generic tools. We anticipate that iProt-Sub will be a powerful tool for proteome-wide prediction of protease-specific substrates and their cleavage sites, and will facilitate hypothesis-driven functional interrogation of protease-specific substrate cleavage and proteolytic events.

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“…Using PseAAC successfully for finding solutions to various problems relevant to peptide/protein sequences, encouraged the idea to introduce PseKNC (Pseudo K-tuple Nucleotide Composition) [38] for generating different feature vectors for DNA/RNA sequences [39], [40] which proved very effective and efficient as well. In recent times a useful, efficient and a very powerful web server called 'Pse-in-One' [41] and its recently updated version 'Pse-in-One2.0' [42] were developed that are able to generate any preferred feature vector of pseudo components for DNA/RNA and protein/peptide sequences according to the requirements of study by any researcher.…”

Section: Feature Extractionmentioning

confidence: 99%

EnhancerP-2L: A Gene regulatory site identification tool for DNA enhancer region using CREs motifs

Ah¹,

Alkhalaf

Iqbal

et al. 2020

Preprint

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Enhancers are DNA fragments that do not encode RNA molecules and proteins, but they act critically in the production of RNAs and proteins by controlling gene expression. Prediction of enhancers and their strength plays significant role in regulating gene expression. Prediction of enhancer regions, in sequences of DNA, is considered a difficult task due to the fact that they are not close to the target gene, have less common motifs and are mostly tissue/cell specific. In recent past, several bioinformatics tools were developed to discriminate enhancers from other regulatory elements and to identify their strengths as well.However the need for improvement in the quality of its prediction method requires enhancements in its application value practically. In this study, we proposed a new method that builds on nucleotide composition and statistical moment based features to distinguish between enhancers and non-enhancers and additionally determine their strength. Our proposed method achieved accuracy better than current state-of-the-art methods using 5-fold and 10-fold cross-validation. The outcomes from our proposed method suggest that the use of statistical moments based features could bear more efficient and effective results. For the accessibility of the scientific community, we have developed a user-friendly web server for EnhancerP-2L which will increase the impact of bioinformatics on medicinal chemistry and drive medical science into an unprecedented resolution. Web server is freely accessible at http://www.biopred.org/enpred.

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Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences

Cited by 127 publications

References 223 publications

Sequence and structure‐based characterization of ubiquitination sites in human and yeast proteins using Chou's sample formulation

Sequence and structure‐based characterization of ubiquitination sites in human and yeast proteins using Chou's sample formulation

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

EnhancerP-2L: A Gene regulatory site identification tool for DNA enhancer region using CREs motifs

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