Rohs R - Search Results

1

DNAproDB: an updated database for the automated and interactive analysis of protein-DNA complexes.

Mitra R, Cohen AS, Sagendorf JM, Berman HM, Rohs R. Mitra R, et al. Among authors: rohs r. Nucleic Acids Res. 2024 Nov 4:gkae970. doi: 10.1093/nar/gkae970. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39494533

2

DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.

Sagendorf JM, Berman HM, Rohs R. Sagendorf JM, et al. Among authors: rohs r. Nucleic Acids Res. 2017 Jul 3;45(W1):W89-W97. doi: 10.1093/nar/gkx272. Nucleic Acids Res. 2017. PMID: 28431131 Free PMC article.

3

Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.

Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD. Azad RN, et al. Among authors: rohs r. Nucleic Acids Res. 2018 Mar 16;46(5):2636-2647. doi: 10.1093/nar/gky033. Nucleic Acids Res. 2018. PMID: 29390080 Free PMC article.

4

DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes.

Sagendorf JM, Markarian N, Berman HM, Rohs R. Sagendorf JM, et al. Among authors: rohs r. Nucleic Acids Res. 2020 Jan 8;48(D1):D277-D287. doi: 10.1093/nar/gkz889. Nucleic Acids Res. 2020. PMID: 31612957 Free PMC article.

5

RNAscape: geometric mapping and customizable visualization of RNA structure.

Mitra R, Cohen AS, Rohs R. Mitra R, et al. Among authors: rohs r. Nucleic Acids Res. 2024 Jul 5;52(W1):W354-W361. doi: 10.1093/nar/gkae269. Nucleic Acids Res. 2024. PMID: 38630617 Free PMC article.

6

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.

Li J, Sagendorf JM, Chiu TP, Pasi M, Perez A, Rohs R. Li J, et al. Among authors: rohs r. Nucleic Acids Res. 2017 Dec 15;45(22):12877-12887. doi: 10.1093/nar/gkx1145. Nucleic Acids Res. 2017. PMID: 29165643 Free PMC article.

7

Crystal Structures of Ternary Complexes of MEF2 and NKX2-5 Bound to DNA Reveal a Disease Related Protein-Protein Interaction Interface.

Lei X, Zhao J, Sagendorf JM, Rajashekar N, Xu J, Dantas Machado AC, Sen C, Rohs R, Feng P, Chen L. Lei X, et al. Among authors: rohs r. J Mol Biol. 2020 Sep 4;432(19):5499-5508. doi: 10.1016/j.jmb.2020.07.004. Epub 2020 Jul 15. J Mol Biol. 2020. PMID: 32681840 Free PMC article.

8

Geometric deep learning of protein-DNA binding specificity.

Mitra R, Li J, Sagendorf JM, Jiang Y, Cohen AS, Chiu TP, Glasscock CJ, Rohs R. Mitra R, et al. Among authors: rohs r. Nat Methods. 2024 Sep;21(9):1674-1683. doi: 10.1038/s41592-024-02372-w. Epub 2024 Aug 5. Nat Methods. 2024. PMID: 39103447 Free PMC article.

9

Structure-based prediction of protein-nucleic acid binding using graph neural networks.

Sagendorf JM, Mitra R, Huang J, Chen XS, Rohs R. Sagendorf JM, et al. Among authors: rohs r. Biophys Rev. 2024 Jun 26;16(3):297-314. doi: 10.1007/s12551-024-01201-w. eCollection 2024 Jun. Biophys Rev. 2024. PMID: 39345796 Free PMC article. Review.

10

Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.

Jiang Y, Chiu TP, Mitra R, Rohs R. Jiang Y, et al. Among authors: rohs r. Biophys J. 2024 Jan 16;123(2):248-259. doi: 10.1016/j.bpj.2023.12.013. Epub 2023 Dec 21. Biophys J. 2024. PMID: 38130056 Free article.

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