The adenovirus DNA-binding protein DBP. [PDF]
J VirolAdenoviruses are a group of double-stranded DNA viruses that can mainly cause respiratory, gastrointestinal, and eye infections in humans. In addition, adenoviruses are employed as vector vaccines for combatting viral infections, including SARS-CoV-2, and serve as excellent gene therapy vectors.
Bertzbach LD +5 more
europepmc +3 more sources
Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein [PDF]
Nature CommunicationsDNA-protein interactions exert the fundamental structure of many pivotal biological processes, such as DNA replication, transcription, and gene regulation. However, accurate and efficient computational methods for identifying these interactions are still
Wenwu Zeng +4 more
doaj +2 more sources
Turning on Protein Function Inhibited by DNA Aptamers Employing a Covalent DNA-Binding Protein [PDF]
ACS Nanoscience AuTakeru Kanazu +6 more
doaj +2 more sources
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. [PDF]
PLoS Computational Biology, 2015 Recent genome-wide experiments in different eukaryotic genomes provide an unprecedented view of transcription factor (TF) binding locations and of nucleosome occupancy.
Ariel Afek +4 more
doaj +1 more source
From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions. [PDF]
PLoS Computational Biology, 2009 DNA-protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA-protein interactions is a challenging problem. Here, we present a
Mu Gao, Jeffrey Skolnick
doaj +1 more source
Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models. [PDF]
PLoS Computational Biology, 2014 DNA binding proteins efficiently search for their cognitive sites on long genomic DNA by combining 3D diffusion and 1D diffusion (sliding) along the DNA.
Tadashi Ando, Jeffrey Skolnick
doaj +1 more source
A novel prediction method for protein DNA-binding residues based on neighboring residue correlations
Biotechnology & Biotechnological Equipment, 2022 Accurately identifying the protein DNA-binding residues is important for understanding the protein–DNA recognition mechanism and protein function annotation.
Jiazhi Song, Guixia Liu, Jingqing Jiang
doaj +1 more source
Facilitated Diffusion of DNA-Binding Proteins [PDF]
Physical Review Letters, 2006 4 pages, 2 figures Nov 22 2005 - accepted for ...
Klenin, K. V. +3 more
openaire +4 more sources
A threading-based method for the prediction of DNA-binding proteins with application to the human genome. [PDF]
PLoS Computational Biology, 2009 Diverse mechanisms for DNA-protein recognition have been elucidated in numerous atomic complex structures from various protein families. These structural data provide an invaluable knowledge base not only for understanding DNA-protein interactions, but ...
Mu Gao, Jeffrey Skolnick
doaj +1 more source
Frontiers in Bioengineering and Biotechnology, 2022 Identification of protein–ligand binding sites plays a critical role in drug discovery. However, there is still a lack of targeted drug prediction for DNA-binding proteins. This study aims at the binding sites of DNA-binding proteins and drugs, by mining
Wei Wang +7 more
doaj +1 more source