Sagendorf J - Search Results

1

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.

2

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.

Vallat B, Webb BM, Westbrook JD, Goddard TD, Hanke CA, Graziadei A, Peisach E, Zalevsky A, Sagendorf J, Tangmunarunkit H, Voinea S, Sekharan M, Yu J, Bonvin AAMJJ, DiMaio F, Hummer G, Meiler J, Tajkhorshid E, Ferrin TE, Lawson CL, Leitner A, Rappsilber J, Seidel CAM, Jeffries CM, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S, Schwede T, Trewhella J, Kesselman C, Berman HM, Sali A. Vallat B, et al. Among authors: sagendorf j. J Mol Biol. 2024 Mar 18:168546. doi: 10.1016/j.jmb.2024.168546. Online ahead of print. J Mol Biol. 2024. PMID: 38508301 Free article.

3

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.

4

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.

5

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.

6

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: sagendorf jm. Nucleic Acids Res. 2018 Mar 16;46(5):2636-2647. doi: 10.1093/nar/gky033. Nucleic Acids Res. 2018. PMID: 29390080 Free PMC article.

7

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.

8

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.

9

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.

10

Direct atom-by-atom chemical identification of nanostructures and defects of topological insulators.

Jiang Y, Wang Y, Sagendorf J, West D, Kou X, Wei X, He L, Wang KL, Zhang S, Zhang Z. Jiang Y, et al. Among authors: sagendorf j. Nano Lett. 2013 Jun 12;13(6):2851-6. doi: 10.1021/nl401186d. Nano Lett. 2013. PMID: 23713705

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