Single-stranded and double-stranded DNA-binding protein prediction using HMM profiles

DNA-binding proteins often play important role in various processes within the cell. Over the last decade, a wide range of classification algorithms and feature extraction techniques have been used to solve this problem. In this paper, we propose a novel DNA-binding protein prediction method called HMMBinder. HMMBinder uses monogram and bigram features extracted from the HMM profiles of the protein sequences. To the best of our knowledge, this is the first application of HMM profile based features for the DNA-binding protein prediction problem. We applied Support Vector Machines (SVM) as a classification technique in HMMBinder. Our method was tested on standard benchmark datasets. We experimentally show that our method outperforms the state-of-the-art methods found in the literature.

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DNA-Binding Protein Prediction Based on Deep Learning Feature Fusion

Intelligent Computing Theories and Application - Lecture Notes in Computer Science ◽

10.1007/978-3-030-84532-2_56 ◽

2021 ◽

pp. 627-633

Author(s):

Shixuan Guan ◽

Tengsheng Jiang ◽

Weizhong Lu ◽

Qiming Fu ◽

Haiou Li ◽

...

Keyword(s):

Deep Learning ◽

Dna Binding ◽

Feature Fusion ◽

Binding Protein ◽

Dna Binding Protein ◽

Protein Prediction

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Preliminary crystallographic studies of the double-stranded DNA-binding protein Sso10b fromSulfolobus solfataricus

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444901015517 ◽

2001 ◽

Vol 57 (12) ◽

pp. 1893-1894 ◽

Cited By ~ 3

Author(s):

Ben N. Wardleworth ◽

Rupert J. M. Russell ◽

Malcolm F. White ◽

Garry L. Taylor

Keyword(s):

Dna Binding ◽

Binding Protein ◽

Dna Binding Protein ◽

Double Stranded Dna

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Herpes Simplex Virus Type 1 Single-Strand DNA Binding Protein ICP8 Enhances the Nuclease Activity of the UL12 Alkaline Nuclease by Increasing Its Processivity

Journal of Virology ◽

10.1128/jvi.79.14.9356-9358.2005 ◽

2005 ◽

Vol 79 (14) ◽

pp. 9356-9358 ◽

Cited By ~ 16

Author(s):

Nina Bacher Reuven ◽

Sandra K. Weller

Keyword(s):

Herpes Simplex Virus ◽

Herpes Simplex ◽

Dna Binding ◽

Herpes Simplex Virus Type ◽

Binding Protein ◽

Dna Binding Protein ◽

Strand Exchange ◽

Double Stranded Dna ◽

Simplex Virus

ABSTRACT UL12 is a 5′- to 3′-exonuclease encoded by herpes simplex virus type 1 (HSV-1) which degrades single- and double-stranded DNA. UL12 and the single-strand DNA binding protein ICP8 mediate a strand exchange reaction. We found that ICP8 inhibited UL12 digestion of single-stranded DNA but stimulated digestion of double-stranded DNA threefold. The stimulatory effect of ICP8 was independent of a strand exchange reaction; furthermore, the effect was specific to ICP8, as it could not be reproduced by Escherichia coli single-stranded DNA binding protein. The effect of ICP8 on the rate of UL12 double-stranded DNA digestion is attributable to an increase in processivity in the presence of ICP8.

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