Boosting the Prediction and Understanding of DNA-binding Domains from Sequence

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Feb 17

PMID 20156993

Citations 21

Authors

Robert E Langlois

Hui Lu

Affiliations

Soon will be listed here.

Abstract

DNA-binding proteins perform vital functions related to transcription, repair and replication. We have developed a new sequence-based machine learning protocol to identify DNA-binding proteins. We compare our method with an extensive benchmark of previously published structure-based machine learning methods as well as a standard sequence alignment technique, BLAST. Furthermore, we elucidate important feature interactions found in a learned model and analyze how specific rules capture general mechanisms that extend across DNA-binding motifs. This analysis is carried out using the malibu machine learning workbench available at http://proteomics.bioengr.uic.edu/malibu and the corresponding data sets and features are available at http://proteomics.bioengr.uic.edu/dna.

Citing Articles

Benchmarking recent computational tools for DNA-binding protein identification.

Luo X, Chi A, Lin A, Ong T, Wong L, Rahman C Brief Bioinform. 2024; 26(1).

PMID: 39657630 PMC: 11630855. DOI: 10.1093/bib/bbae634.

ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.

Pradhan U, Meher P, Naha S, Das R, Gupta A, Parsad R Protein Sci. 2024; 33(6):e5015.

PMID: 38747369 PMC: 11094783. DOI: 10.1002/pro.5015.

DNAPred_Prot: Identification of DNA-Binding Proteins Using Composition- and Position-Based Features.

Barukab O, Khan Y, Khan S, Chou K Appl Bionics Biomech. 2022; 2022:5483115.

PMID: 35465187 PMC: 9020926. DOI: 10.1155/2022/5483115.

PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method.

Wang J, Zheng H, Yang Y, Xiao W, Liu T Biomed Res Int. 2020; 2020:7297631.

PMID: 32352006 PMC: 7174956. DOI: 10.1155/2020/7297631.

HMMPred: Accurate Prediction of DNA-Binding Proteins Based on HMM Profiles and XGBoost Feature Selection.

Sang X, Xiao W, Zheng H, Yang Y, Liu T Comput Math Methods Med. 2020; 2020:1384749.

PMID: 32300371 PMC: 7142336. DOI: 10.1155/2020/1384749.

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