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- Tianyin Zhou, Lin Yang, +5 authors Remo Rohs
- Nucleic Acids Research
- 2013
We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA… (More)
- Yongheng Chen, Darren L Bates, +5 authors Lin Chen
- Cell reports
- 2012
GATA transcription factors regulate transcription during development and differentiation by recognizing distinct GATA sites with a tandem of two conserved zinc fingers, and by mediating long-range… (More)
- Yao-Chuan Chang, Meng Xu, Ana Carolina Dantas Machado, Xian Jessica Yu, Remo Rohs, Xiaojiang S. Chen
- Cell reports
- 2013
The DNA tumor virus Simian virus 40 (SV40) is a model system for studying eukaryotic replication. SV40 large tumor antigen (LTag) is the initiator/helicase that is essential for genome replication.… (More)
- Zengqin Deng, Qing Wang, +16 authors Zhongzhou Chen
- Nature communications
- 2015
Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain… (More)
- Ana Carolina Dantas Machado, Skyler B. Saleebyan, +9 authors Remo Rohs
- Biochemistry and molecular biology education : a…
- 2012
3D visualization assists in identifying diverse mechanisms of protein-DNA recognition that can be observed for transcription factors and other DNA binding proteins. We used Proteopedia to illustrate… (More)
Proteins and DNA form complexes due to complementary properties of their molecular structure and electrostatic potential at the binding interface. While proteins predominantly consist of globular… (More)
- Remo Rohs, Ana Carolina Dantas Machado, Lin Yang
- Nature Structural &Molecular Biology
- 2015
Sex-determining transcription factors recognize their genomic target sites through mechanisms of DNA base-and-shape readout in combination with cooperative binding. Murphy et al. reveal that for one… (More)
- Xiaojun Zhang, Ana Carolina Dantas Machado, +10 authors Likai Song
- 2019
- Allan Lazarovici, Tianyin Zhou, +7 authors Harmen J. Bussemaker
- 2013
DNA binding proteins find their cognate sequences within genomic DNA through recognition of specific chemical and structural features. Here, we demonstrate that high-resolution DNase I cleavage… (More)
Various biological processes are driven by interactions between proteins and their DNA-binding sites. To achieve DNA-binding specificity, an interplay between base and shape readout modes by proteins… (More)
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