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Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations.
Nucleic Acids Res. 2018 Mar 16;46(5):2636-2647. doi: 10.1093/nar/gky033.
Nucleic Acids Res. 2018.
PMID: 29390080
Free PMC article.
DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.
Sagendorf JM, Berman HM, Rohs R.
Sagendorf JM, et al.
Nucleic Acids Res. 2017 Jul 3;45(W1):W89-W97. doi: 10.1093/nar/gkx272.
Nucleic Acids Res. 2017.
PMID: 28431131
Free PMC article.
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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: sagendorf jm.
Nucleic Acids Res. 2017 Dec 15;45(22):12877-12887. doi: 10.1093/nar/gkx1145.
Nucleic Acids Res. 2017.
PMID: 29165643
Free PMC article.
Item in Clipboard
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.
Nucleic Acids Res. 2020 Jan 8;48(D1):D277-D287. doi: 10.1093/nar/gkz889.
Nucleic Acids Res. 2020.
PMID: 31612957
Free PMC article.
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Structure of the Forkhead Domain of FOXA2 Bound to a Complete DNA Consensus Site.
Li J, Dantas Machado AC, Guo M, Sagendorf JM, Zhou Z, Jiang L, Chen X, Wu D, Qu L, Chen Z, Chen L, Rohs R, Chen Y.
Li J, et al. Among authors: sagendorf jm.
Biochemistry. 2017 Jul 25;56(29):3745-3753. doi: 10.1021/acs.biochem.7b00211. Epub 2017 Jul 11.
Biochemistry. 2017.
PMID: 28644006
Free PMC article.
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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: sagendorf jm.
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.
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PNAbind: 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.
bioRxiv [Preprint]. 2024 Mar 2:2024.02.27.582387. doi: 10.1101/2024.02.27.582387.
bioRxiv. 2024.
PMID: 38529493
Free PMC article.
Preprint.
Item in Clipboard
DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity.
Mitra R, Li J, Sagendorf JM, Jiang Y, Chiu TP, Rohs R.
Mitra R, et al. Among authors: sagendorf jm.
bioRxiv [Preprint]. 2023 Dec 16:2023.12.15.571942. doi: 10.1101/2023.12.15.571942.
bioRxiv. 2023.
PMID: 38293168
Free PMC article.
Preprint.
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