Multiscale simulations of DNA from electrons to nucleosomes
Abstract This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-
dimensional structural and dynamic information encoded in DNA sequences and introduces …
dimensional structural and dynamic information encoded in DNA sequences and introduces …
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences
Computational prediction of nucleic acid-binding residues in protein sequences is an active
field of research, with over 80 methods that were released in the past 2 decades. We identify …
field of research, with over 80 methods that were released in the past 2 decades. We identify …
PDNAPred: Interpretable prediction of protein-DNA binding sites based on pre-trained protein language models
L Zhang, T Liu - International Journal of Biological Macromolecules, 2024 - Elsevier
Protein-DNA interactions play critical roles in various biological processes and are essential
for drug discovery. However, traditional experimental methods are labor-intensive and …
for drug discovery. However, traditional experimental methods are labor-intensive and …
DNAproDB: an updated database for the automated and interactive analysis of protein–DNA complexes
R Mitra, AS Cohen, JM Sagendorf… - Nucleic Acids …, 2025 - academic.oup.com
Abstract DNAproDB (https://dnaprodb. usc. edu/) is a database, visualization tool, and
processing pipeline for analyzing structural features of protein–DNA interactions. Here, we …
processing pipeline for analyzing structural features of protein–DNA interactions. Here, we …