Sequence-based protein domain boundary prediction using BP neural network with various property profiles

2008 ◽  
Vol 71 (1) ◽  
pp. 300-307 ◽  
Author(s):  
Lei Ye ◽  
Ting Liu ◽  
Zhaohui Wu ◽  
Ruhong Zhou
Keyword(s):  
Neural Network ◽  
Bp Neural Network ◽  
Domain Boundary ◽  
Protein Domain ◽  
Domain Boundary Prediction

DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network

2019 ◽  
Vol 35 (24) ◽  
pp. 5128-5136 ◽  
Author(s):  
Qiang Shi ◽  
Weiya Chen ◽  
Siqi Huang ◽  
Fanglin Jin ◽  
Yinghao Dong ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Structure Prediction ◽  
Domain Boundary ◽  
Protein Domain ◽  
Supplementary Information ◽  
High Dimensions ◽  
Long Range Interactions ◽  
Domain Boundary Prediction ◽  
And Function

Abstract Motivation Accurate delineation of protein domain boundary plays an important role for protein engineering and structure prediction. Although machine-learning methods are widely used to predict domain boundary, these approaches often ignore long-range interactions among residues, which have been proven to improve the prediction performance. However, how to simultaneously model the local and global interactions to further improve domain boundary prediction is still a challenging problem. Results This article employs a hybrid deep learning method that combines convolutional neural network and gate recurrent units’ models for domain boundary prediction. It not only captures the local and non-local interactions, but also fuses these features for prediction. Additionally, we adopt balanced Random Forest for classification to deal with high imbalance of samples and high dimensions of deep features. Experimental results show that our proposed approach (DNN-Dom) outperforms existing machine-learning-based methods for boundary prediction. We expect that DNN-Dom can be useful for assisting protein structure and function prediction. Availability and implementation The method is available as DNN-Dom Server at http://isyslab.info/DNN-Dom/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Improved general regression network for protein domain boundary prediction

2008 ◽  
Vol 9 (S1) ◽  
Author(s):  
Paul D Yoo ◽  
Abdur R Sikder ◽  
Bing Bing Zhou ◽  
Albert Y Zomaya
Keyword(s):  
Domain Boundary ◽  
Protein Domain ◽  
Domain Boundary Prediction ◽  
General Regression

DomNet: Protein Domain Boundary Prediction Using Enhanced General Regression Network and New Profiles

2008 ◽  
Vol 7 (2) ◽  
pp. 172-181 ◽  
Author(s):  
Paul D. Yoo ◽  
Abdur R. Sikder ◽  
Javid Taheri ◽  
Bing Bing Zhou ◽  
Albert Y. Zomaya
Keyword(s):  
Domain Boundary ◽  
Protein Domain ◽  
Domain Boundary Prediction ◽  
General Regression

Protein Domain Boundary Prediction Using Multiple Protein Properties

2013 ◽  
Vol 7 (1) ◽  
pp. 104-109
Author(s):  
Jiaxin Wang ◽  
Jiafeng Wang ◽  
Wei Du ◽  
Chong Yu ◽  
Yanchun Liang
Keyword(s):  
Domain Boundary ◽  
Protein Domain ◽  
Multiple Protein ◽  
Protein Properties ◽  
Domain Boundary Prediction

PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier

2015 ◽  
pp. 441-450 ◽  
Author(s):  
Piyali Chatterjee ◽  
Subhadip Basu ◽  
Julian Zubek ◽  
Mahantapas Kundu ◽  
Mita Nasipuri ◽  
...  
Keyword(s):  
Random Forest ◽  
Domain Boundary ◽  
Random Forest Classifier ◽  
Protein Domain ◽  
Domain Boundary Prediction

scholarly journals DomBpred: protein domain boundary predictor using inter-residue distance and domain-residue level clustering

2021 ◽  
Author(s):  
Zhongze Yu ◽  
Chunxiang Peng ◽  
Jun Liu ◽  
Biao Zhang ◽  
Xiaogen Zhou ◽  
...  
Keyword(s):  
Clustering Algorithm ◽  
State Of The Art ◽  
Domain Boundary ◽  
Residue Level ◽  
Single Domain ◽  
Protein Domain ◽  
Test Set ◽  
Cut Points ◽  
Domain Boundary Prediction ◽  
Domain Protein

Domain boundary prediction is one of the most important problems in the study of protein structure and function, especially for large proteins. At present, most domain boundary prediction methods have low accuracy and limitations in dealing with multi-domain proteins. In this study, we develop a sequence-based protein domain boundary predictor, named DomBpred. In DomBpred, the input sequence is firstly classified as either a single-domain protein or a multi-domain protein through a designed effective sequence metric based on a constructed single-domain sequence library. For the multi-domain protein, a domain-residue level clustering algorithm inspired by Ising model is proposed to cluster the spatially close residues according inter-residue distance. The unclassified residues and the residues at the edge of the cluster are then tuned by the secondary structure to form potential cut points. Finally, a domain boundary scoring function is proposed to recursively evaluate the potential cut points to generate the domain boundary. DomBpred is tested on a large-scale test set of FUpred comprising 2549 proteins. Experimental results show that DomBpred better performs than the state-of-the-art methods in classifying whether protein sequences are composed by single or multiple domains, and the Matthew's correlation coefficient is 0.882. Moreover, on 849 multi-domain proteins, the domain boundary distance and normalised domain overlap scores of DomBpred are 0.523 and 0.824, respectively, which are 5.0% and 4.2% higher than those of the best comparison method, respectively. Comparison with other methods on the given test set shows that DomBpred outperforms most state-of-the-art sequence-based methods and even achieves better results than the top-level template-based method.

Computer-Assisted Protein Domain Boundary Prediction Using the Dom-Pred Server

2007 ◽  
Vol 8 (2) ◽  
pp. 181-188 ◽  
Author(s):  
Kevin Bryson ◽  
Domenico Cozzetto ◽  
David Jones
Keyword(s):  
Domain Boundary ◽  
Protein Domain ◽  
Computer Assisted ◽  
Domain Boundary Prediction

ConDo: protein domain boundary prediction using coevolutionary information

2018 ◽  
Vol 35 (14) ◽  
pp. 2411-2417 ◽  
Author(s):  
Seung Hwan Hong ◽  
Keehyoung Joo ◽  
Jooyoung Lee
Keyword(s):  
Long Range ◽  
Domain Boundary ◽  
Prediction Method ◽  
Protein Domain ◽  
Supplementary Information ◽  
Sequence Information ◽  
Multiple Sequence ◽  
Domain Boundary Prediction ◽  
Correlation Information ◽  
And Function

AbstractMotivationDomain boundary prediction is one of the most important problems in the study of protein structure and function. Many sequence-based domain boundary prediction methods are either template-based or machine learning (ML) based. ML-based methods often perform poorly due to their use of only local (i.e. short-range) features. These conventional features such as sequence profiles, secondary structures and solvent accessibilities are typically restricted to be within 20 residues of the domain boundary candidate.ResultsTo address the performance of ML-based methods, we developed a new protein domain boundary prediction method (ConDo) that utilizes novel long-range features such as coevolutionary information in addition to the aforementioned local window features as inputs for ML. Toward this purpose, two types of coevolutionary information were extracted from multiple sequence alignment using direct coupling analysis: (i) partially aligned sequences, and (ii) correlated mutation information. Both the partially aligned sequence information and the modularity of residue–residue couplings possess long-range correlation information.Availability and implementationhttps://github.com/gicsaw/ConDo.gitSupplementary informationSupplementary data are available at Bioinformatics online.

An Improved Profile-Level Domain Linker Propensity Index for Protein Domain Boundary Prediction.

2011 ◽  
Vol 18 (1) ◽  
pp. 7-16 ◽  
Author(s):  
Yanfeng Zhang ◽  
Bin Liu ◽  
Qiwen Dong ◽  
Victor X. Jin
Keyword(s):  
Domain Boundary ◽  
Protein Domain ◽  
Domain Boundary Prediction
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