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Page 1
AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities.
Fleming J, Magana P, Nair S, Tsenkov M, Bertoni D, Pidruchna I, Lima Afonso MQ, Midlik A, Paramval U, Žídek A, Laydon A, Kovalevskiy O, Pan J, Cheng J, Avsec Ž, Bycroft C, Wong LH, Last M, Mirdita M, Steinegger M, Kohli P, Váradi M, Velankar S. Fleming J, et al. Among authors: zidek a. J Mol Biol. 2025 Aug 1;437(15):168967. doi: 10.1016/j.jmb.2025.168967. Epub 2025 Jan 29. J Mol Biol. 2025. PMID: 40133787 Free article.
Gestational exposure to environmental chemical mixtures and cognitive abilities in children: A pooled analysis of two North American birth cohorts.
Puvvula J, Hwang WT, McCandless L, Xie C, Braun JM, Vuong AM, Oulhote Y, Schisterman EF, Shinohara RT, Booij L, Bouchard MF, Linn K, Borghese MM, Seguin JR, Zidek A, Till C, Fraser W, Yolton K, Cecil KM, Ashley-Martin J, Arbuckle TE, Lanphear B, Chen A. Puvvula J, et al. Among authors: zidek a. Environ Int. 2025 Feb;196:109298. doi: 10.1016/j.envint.2025.109298. Epub 2025 Jan 29. Environ Int. 2025. PMID: 39893913 Free PMC article.
Addendum: Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. Abramson J, et al. Among authors: zidek a. Nature. 2024 Dec;636(8042):E4. doi: 10.1038/s41586-024-08416-7. Nature. 2024. PMID: 39604737 Free PMC article. No abstract available.
Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, Ronneberger O, Willmore L, Ballard AJ, Bambrick J, Bodenstein SW, Evans DA, Hung CC, O'Neill M, Reiman D, Tunyasuvunakool K, Wu Z, Žemgulytė A, Arvaniti E, Beattie C, Bertolli O, Bridgland A, Cherepanov A, Congreve M, Cowen-Rivers AI, Cowie A, Figurnov M, Fuchs FB, Gladman H, Jain R, Khan YA, Low CMR, Perlin K, Potapenko A, Savy P, Singh S, Stecula A, Thillaisundaram A, Tong C, Yakneen S, Zhong ED, Zielinski M, Žídek A, Bapst V, Kohli P, Jaderberg M, Hassabis D, Jumper JM. Abramson J, et al. Among authors: zidek a. Nature. 2024 Jun;630(8016):493-500. doi: 10.1038/s41586-024-07487-w. Epub 2024 May 8. Nature. 2024. PMID: 38718835 Free PMC article.
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.
Varadi M, Bertoni D, Magana P, Paramval U, Pidruchna I, Radhakrishnan M, Tsenkov M, Nair S, Mirdita M, Yeo J, Kovalevskiy O, Tunyasuvunakool K, Laydon A, Žídek A, Tomlinson H, Hariharan D, Abrahamson J, Green T, Jumper J, Birney E, Steinegger M, Hassabis D, Velankar S. Varadi M, et al. Among authors: zidek a. Nucleic Acids Res. 2024 Jan 5;52(D1):D368-D375. doi: 10.1093/nar/gkad1011. Nucleic Acids Res. 2024. PMID: 37933859 Free PMC article.
Cohort profile update: The Canadian Maternal-Infant Research on Environmental Chemicals Child Development study (MIREC-CD PLUS).
Fisher M, Muckle G, Lanphear B, Arbuckle TE, Braun JM, Zidek A, Vélez MP, Lupien N, Bastien S, Ashley-Martin J, Oulhote Y, Borghese MM, Walker M, Asztalos E, Bouchard MF, Booij L, Palmert MR, Morrison KM, Cummings EA, Khatchadourian K, Panagiotopoulos C, Glendon G, Shutt R, Abdul-Fatah A, Seal K, Fraser WD. Fisher M, et al. Among authors: zidek a. Paediatr Perinat Epidemiol. 2023 Nov;37(8):719-732. doi: 10.1111/ppe.13013. Epub 2023 Nov 3. Paediatr Perinat Epidemiol. 2023. PMID: 37921434
Remotely Supervised Weight Loss and Exercise Training to Improve Rheumatoid Arthritis Cardiovascular Risk: Rationale and Design of the Supervised Weight Loss Plus Exercise Training-Rheumatoid Arthritis Trial.
Andonian B, Ross LM, Zidek AM, Fos LB, Piner LW, Johnson JL, Belski KB, Counts JD, Pieper CF, Siegler IC, Bales CW, Porter Starr KN, Kraus WE, Huffman KM. Andonian B, et al. Among authors: zidek am. ACR Open Rheumatol. 2023 May;5(5):252-263. doi: 10.1002/acr2.11536. Epub 2023 Mar 29. ACR Open Rheumatol. 2023. PMID: 36992545 Free PMC article. Review.
ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. Vallat B, et al. Among authors: zidek a. J Mol Biol. 2023 Jul 15;435(14):168021. doi: 10.1016/j.jmb.2023.168021. Epub 2023 Feb 23. J Mol Biol. 2023. PMID: 36828268 Free PMC article.
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, Laydon A, Molodenskiy D, Piovesan D, Salladini E, Salzberg SL, Sommer MJ, Steinegger M, Suhajda E, Svergun D, Tenorio-Ku L, Tosatto S, Tunyasuvunakool K, Waterhouse AM, Žídek A, Schwede T, Orengo C, Velankar S. Varadi M, et al. Among authors: zidek a. Gigascience. 2022 Nov 30;11:giac118. doi: 10.1093/gigascience/giac118. Gigascience. 2022. PMID: 36448847 Free PMC article.
The chemical landscape of high-throughput new approach methodologies for exposure.
Isaacs KK, Egeghy P, Dionisio KL, Phillips KA, Zidek A, Ring C, Sobus JR, Ulrich EM, Wetmore BA, Williams AJ, Wambaugh JF. Isaacs KK, et al. Among authors: zidek a. J Expo Sci Environ Epidemiol. 2022 Nov;32(6):820-832. doi: 10.1038/s41370-022-00496-9. Epub 2022 Nov 26. J Expo Sci Environ Epidemiol. 2022. PMID: 36435938 Free PMC article. Review.
25 results