Si D - Search Results

1

DeepTracer-ID: De novo protein identification from cryo-EM maps.

Chang L, Wang F, Connolly K, Meng H, Su Z, Cvirkaite-Krupovic V, Krupovic M, Egelman EH, Si D. Chang L, et al. Among authors: si d. Biophys J. 2022 Aug 2;121(15):2840-2848. doi: 10.1016/j.bpj.2022.06.025. Epub 2022 Jun 28. Biophys J. 2022. PMID: 35769006 Free PMC article.

2

Tracing beta strands using StrandTwister from cryo-EM density maps at medium resolutions.

Si D, He J. Si D, et al. Structure. 2014 Nov 4;22(11):1665-76. doi: 10.1016/j.str.2014.08.017. Epub 2014 Oct 9. Structure. 2014. PMID: 25308866 Free article.

3

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.

Si D, He J. Si D, et al. Biomed Res Int. 2017;2017:1793213. doi: 10.1155/2017/1793213. Epub 2017 Jan 10. Biomed Res Int. 2017. PMID: 28164115 Free PMC article.

4

Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing.

Ng A, Si D. Ng A, et al. Among authors: si d. J Comput Biol. 2018 Mar;25(3):326-336. doi: 10.1089/cmb.2017.0155. Epub 2017 Oct 16. J Comput Biol. 2018. PMID: 29035579

5

Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps ^†.

Avramov TK, Vyenielo D, Gomez-Blanco J, Adinarayanan S, Vargas J, Si D. Avramov TK, et al. Among authors: si d. Molecules. 2019 Mar 26;24(6):1181. doi: 10.3390/molecules24061181. Molecules. 2019. PMID: 30917528 Free PMC article.

6

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps.

Si D, Moritz SA, Pfab J, Hou J, Cao R, Wang L, Wu T, Cheng J. Si D, et al. Sci Rep. 2020 Mar 9;10(1):4282. doi: 10.1038/s41598-020-60598-y. Sci Rep. 2020. PMID: 32152330 Free PMC article.

7

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes.

Pfab J, Phan NM, Si D. Pfab J, et al. Among authors: si d. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2017525118. doi: 10.1073/pnas.2017525118. Proc Natl Acad Sci U S A. 2021. PMID: 33361332 Free PMC article.

8

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Lawson CL, et al. Among authors: si d. Nat Methods. 2021 Feb;18(2):156-164. doi: 10.1038/s41592-020-01051-w. Epub 2021 Feb 4. Nat Methods. 2021. PMID: 33542514 Free PMC article.

9

Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing.

Wang F, Mustafa K, Suciu V, Joshi K, Chan CH, Choi S, Su Z, Si D, Hochbaum AI, Egelman EH, Bond DR. Wang F, et al. Among authors: si d. Nat Microbiol. 2022 Aug;7(8):1291-1300. doi: 10.1038/s41564-022-01159-z. Epub 2022 Jul 7. Nat Microbiol. 2022. PMID: 35798889 Free PMC article.

10

Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times.

Wang F, Chan CH, Suciu V, Mustafa K, Ammend M, Si D, Hochbaum AI, Egelman EH, Bond DR. Wang F, et al. Among authors: si d. Elife. 2022 Sep 5;11:e81551. doi: 10.7554/eLife.81551. Elife. 2022. PMID: 36062910 Free PMC article.

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