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Phillips M, Malone KL, Boyle BW, Montgomery C, Kressy IA, Joseph FM, Bright KM, Boyson SP, Chang S, Nix JC, Young NL, Jeffers V, Frietze S, Glass KC. Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains. J Med Chem. 2024 May 23;67(10):8186-8200. doi: 10.1021/acs.jmedchem.4c00210. Epub 2024 May 11. PubMed PMID: 38733345; NIHMSID:NIHMS1994696.
Afonine PV, Adams PD, Sobolev OV, Urzhumtsev AG. Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein Sci. 2024 Mar;33(3):e4909. doi: 10.1002/pro.4909. PubMed PMID: 38358136; PubMed Central PMCID: PMC10868464.
Urzhumtsev A, Adams P, Afonine P. Universal parameters of bulk-solvent masks. Acta Crystallogr A Found Adv. 2024 Mar 1;80(Pt 2):194-201. doi: 10.1107/S2053273324000299. Epub 2024 Feb 9. PubMed PMID: 38334174; PubMed Central PMCID: PMC10913670.
Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCrJ. 2024 Mar 1;11(Pt 2):140-151. doi: 10.1107/S2052252524001246. PubMed PMID: 38358351; PubMed Central PMCID: PMC10916293.
Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, Lee TS. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metab Eng. 2024 Mar;82:157-170. doi: 10.1016/j.ymben.2024.02.004. Epub 2024 Feb 16. PubMed PMID: 38369052.
Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Author Correction: Structural evidence for intermediates during O(2) formation in photosystem II. Nature. 2024 Feb;626(7999):E12. doi: 10.1038/s41586-024-07099-4. PubMed PMID: 38291188; PubMed Central PMCID: PMC10866699.
Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, Chakraborty R, Stahl DA, Adams PD, Arkin AP, He Z, Zhou J. Environmental stress mediates groundwater microbial community assembly. Nat Microbiol. 2024 Feb;9(2):490-501. doi: 10.1038/s41564-023-01573-x. Epub 2024 Jan 11. PubMed PMID: 38212658.
Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Res Sq. 2024 Jan 25;. doi: 10.21203/rs.3.rs-3864137/v1. PubMed PMID: 38343795; PubMed Central PMCID: PMC10854310.
Terwilliger TC, Liebschner D, Croll TI, Williams CJ, McCoy AJ, Poon BK, Afonine PV, Oeffner RD, Richardson JS, Read RJ, Adams PD. AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nat Methods. 2024 Jan;21(1):110-116. doi: 10.1038/s41592-023-02087-4. Epub 2023 Nov 30. PubMed PMID: 38036854; PubMed Central PMCID: PMC10776388.
Mendez D, Holton JM, Lyubimov AY, Hollatz S, Mathews II, Cichosz A, Martirosyan V, Zeng T, Stofer R, Liu R, Song J, McPhillips S, Soltis M, Cohen AE. Deep residual networks for crystallography trained on synthetic data. Acta Crystallogr D Struct Biol. 2024 Jan 1;80(Pt 1):26-43. doi: 10.1107/S2059798323010586. Epub 2024 Jan 1. PubMed PMID: 38164955; PubMed Central PMCID: PMC10833344.
Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD. Improved joint X-ray and neutron refinement procedure in Phenix. Acta Crystallogr D Struct Biol. 2023 Dec 1;79(Pt 12):1079-1093. doi: 10.1107/S2059798323008914. Epub 2023 Nov 9. PubMed PMID: 37942718; PubMed Central PMCID: PMC10833352.
Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2. Appl Environ Microbiol. 2023 Oct 31;89(10):e0085223. doi: 10.1128/aem.00852-23. Epub 2023 Sep 19. PubMed PMID: 37724856; PubMed Central PMCID: PMC10617552.
Takasuka TE, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG. Quantitative Analysis of The High-Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem. 2023 Oct 17;24(20):e202300357. doi: 10.1002/cbic.202300357. Epub 2023 Aug 28. PubMed PMID: 37402642.
Afonine PV, Sobolev OV, Moriarty NW, Terwilliger TC, Adams PD. Overall protein structure quality assessment using hydrogen-bonding parameters. Acta Crystallogr D Struct Biol. 2023 Aug 1;79(Pt 8):684-693. doi: 10.1107/S2059798323005077. Epub 2023 Jul 11. PubMed PMID: 37431759; PubMed Central PMCID: PMC10394671.
Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR. A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. Lab Chip. 2023 Jul 25;23(15):3361-3369. doi: 10.1039/d2lc00980c. PubMed PMID: 37401915; PubMed Central PMCID: PMC10484474.
Afonine PV, Adams PD, Urzhumtsev AG. Efficient structure-factor modeling for crystals with multiple components. Acta Crystallogr A Found Adv. 2023 Jul 1;79(Pt 4):345-352. doi: 10.1107/S205327332300356X. Epub 2023 Jun 20. PubMed PMID: 37338214; PubMed Central PMCID: PMC10317137.
Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Bulk-solvent and overall scaling revisited: faster calculations, improved results. Corrigendum. Acta Crystallogr D Struct Biol. 2023 Jul 1;79(Pt 7):666-667. doi: 10.1107/S2059798323004825. Epub 2023 Jun 20. PubMed PMID: 37338421; PubMed Central PMCID: PMC10306067.
Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, Gätcke J, Haupt S, Nangca II, Keable SM, Aydin AO, Tono K, Owada S, Gee LB, Fuller FD, Batyuk A, Alonso-Mori R, Holton JM, Paley DW, Moriarty NW, Mamedov F, Adams PD, Brewster AS, Dobbek H, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yano J, Yachandra VK. Structural evidence for intermediates during O(2) formation in photosystem II. Nature. 2023 May;617(7961):629-636. doi: 10.1038/s41586-023-06038-z. Epub 2023 May 3. PubMed PMID: 37138085; PubMed Central PMCID: PMC10191843.
Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, Hartwig JF, Mukhopadhyay A, Keasling JD. Complete integration of carbene-transfer chemistry into biosynthesis. Nature. 2023 May;617(7960):403-408. doi: 10.1038/s41586-023-06027-2. Epub 2023 May 3. PubMed PMID: 37138074.
Dai J, Wilhelm KB, Bischoff AJ, Pereira JH, Dedeo MT, García-Almedina DM, Adams PD, Groves JT, Francis MB. A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins. Small. 2023 May;19(20):e2207805. doi: 10.1002/smll.202207805. Epub 2023 Feb 21. PubMed PMID: 36811150.
Englund E, Schmidt M, Nava AA, Lechner A, Deng K, Jocic R, Lin Y, Roberts J, Benites VT, Kakumanu R, Gin JW, Chen Y, Liu Y, Petzold CJ, Baidoo EEK, Northen TR, Adams PD, Katz L, Yuzawa S, Keasling JD. Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase. J Am Chem Soc. 2023 Apr 26;145(16):8822-8832. doi: 10.1021/jacs.2c11027. Epub 2023 Apr 14. PubMed PMID: 37057992; PubMed Central PMCID: PMC10141241.
Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun. 2023 Mar 28;14(1):1733. doi: 10.1038/s41467-023-37254-w. PubMed PMID: 36977673; PubMed Central PMCID: PMC10044120.
Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nat Plants. 2023 Mar;9(3):486-500. doi: 10.1038/s41477-023-01358-4. Epub 2023 Feb 27. PubMed PMID: 36849618; PubMed Central PMCID: PMC10115243.
Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD. Accelerating crystal structure determination with iterative AlphaFold prediction. Acta Crystallogr D Struct Biol. 2023 Mar 1;79(Pt 3):234-244. doi: 10.1107/S205979832300102X. Epub 2023 Feb 27. PubMed PMID: 36876433; PubMed Central PMCID: PMC9986801.
Deng K, Wang X, Ing N, Opgenorth P, de Raad M, Kim J, Simmons BA, Adams PD, Singh AK, Lee TS, Northen TR. Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS). Anal Biochem. 2023 Feb 1;662:114997. doi: 10.1016/j.ab.2022.114997. Epub 2022 Nov 24. PubMed PMID: 36435200.
Liebschner D, Moriarty NW, Poon BK, Adams PD. In situ ligand restraints from quantum-mechanical methods. Acta Crystallogr D Struct Biol. 2023 Feb 1;79(Pt 2):100-110. doi: 10.1107/S2059798323000025. Epub 2023 Jan 20. PubMed PMID: 36762856; PubMed Central PMCID: PMC9912925.
Terwilliger TC, Poon BK, Afonine PV, Schlicksup CJ, Croll TI, Millán C, Richardson JS, Read RJ, Adams PD. Improved AlphaFold modeling with implicit experimental information. Nat Methods. 2022 Nov;19(11):1376-1382. doi: 10.1038/s41592-022-01645-6. Epub 2022 Oct 20. PubMed PMID: 36266465; PubMed Central PMCID: PMC9636017.
Oeffner RD, Croll TI, Millán C, Poon BK, Schlicksup CJ, Read RJ, Terwilliger TC. Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE. Acta Crystallogr D Struct Biol. 2022 Nov 1;78(Pt 11):1303-1314. doi: 10.1107/S2059798322010026. Epub 2022 Oct 27. PubMed PMID: 36322415; PubMed Central PMCID: PMC9629492.
Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome. 2022 Oct 25;10(1):183. doi: 10.1186/s40168-022-01377-x. PubMed PMID: 36280858; PubMed Central PMCID: PMC9594917.
Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. Structural plasticity enables evolution and innovation of RuBisCO assemblies. Sci Adv. 2022 Aug 26;8(34):eadc9440. doi: 10.1126/sciadv.adc9440. Epub 2022 Aug 26. PubMed PMID: 36026446; PubMed Central PMCID: PMC9417184.
Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep. 2022 Jul 16;12(1):12197. doi: 10.1038/s41598-022-15930-z. PubMed PMID: 35842458; PubMed Central PMCID: PMC9287821.
Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, Velankar S, Vonrhein C, Waterman DG, Kurisu G, Berman HM, Burley SK, Peisach E. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. J Mol Biol. 2022 Jun 15;434(11):167599. doi: 10.1016/j.jmb.2022.167599. Epub 2022 Apr 20. Review. PubMed PMID: 35460671; PubMed Central PMCID: PMC10292674.
Macdonald SS, Pereira JH, Liu F, Tegl G, DeGiovanni A, Wardman JF, Deutsch S, Yoshikuni Y, Adams PD, Withers SG. A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. ACS Cent Sci. 2022 Apr 27;8(4):430-440. doi: 10.1021/acscentsci.1c01570. Epub 2022 Mar 16. PubMed PMID: 35505869; PubMed Central PMCID: PMC9052796.
Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Garcia Martin H, Singh AK. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. Microsyst Nanoeng. 2022;8:31. doi: 10.1038/s41378-022-00357-3. eCollection 2022. PubMed PMID: 35359611; PubMed Central PMCID: PMC8924257.
Hancock M, Peulen TO, Webb B, Poon B, Fraser JS, Adams P, Sali A. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol. 2022 Mar;214(1):107841. doi: 10.1016/j.jsb.2022.107841. Epub 2022 Feb 9. PubMed PMID: 35149213; PubMed Central PMCID: PMC9278553.
Chen Y, Kaplan Lease N, Gin JW, Ogorzalek TL, Adams PD, Hillson NJ, Petzold CJ. Modular automated bottom-up proteomic sample preparation for high-throughput applications. PLoS One. 2022;17(2):e0264467. doi: 10.1371/journal.pone.0264467. eCollection 2022. PubMed PMID: 35213656; PubMed Central PMCID: PMC8880914.
Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D. Accurate prediction of protein structures and interactions using a three-track neural network. Science. 2021 Aug 20;373(6557):871-876. doi: 10.1126/science.abj8754. Epub 2021 Jul 15. PubMed PMID: 34282049; PubMed Central PMCID: PMC7612213.
van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure. 2021 Aug 5;29(8):913-921.e4. doi: 10.1016/j.str.2021.03.011. Epub 2021 Apr 5. PubMed PMID: 33823127; PubMed Central PMCID: PMC8349848.
Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H, Sauter NK, Adams PD. Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map. Proc Natl Acad Sci U S A. 2021 Jun 15;118(24). doi: 10.1073/pnas.2102342118. PubMed PMID: 34117122; PubMed Central PMCID: PMC8214684.
Ing N, Deng K, Chen Y, Aulitto M, Gin JW, Pham TLM, Petzold CJ, Singer SW, Bowen B, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR. A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities. Sci Rep. 2021 Jun 3;11(1):11803. doi: 10.1038/s41598-021-91181-8. PubMed PMID: 34083602; PubMed Central PMCID: PMC8175421.
Pham LTM, Deng K, Northen TR, Singer SW, Adams PD, Simmons BA, Sale KL. Experimental and theoretical insights into the effects of pH on catalysis of bond-cleavage by the lignin peroxidase isozyme H8 from Phanerochaete chrysosporium. Biotechnol Biofuels. 2021 Apr 29;14(1):108. doi: 10.1186/s13068-021-01953-7. PubMed PMID: 33926536; PubMed Central PMCID: PMC8082889.
Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Ho CM, Li X, Zhou ZH. Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. Acta Crystallogr D Struct Biol. 2021 Apr 1;77(Pt 4):457-462. doi: 10.1107/S2059798321001765. Epub 2021 Mar 30. PubMed PMID: 33825706; PubMed Central PMCID: PMC8025881.
Lui LM, Majumder EL, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol. 2021;12:642422. doi: 10.3389/fmicb.2021.642422. eCollection 2021. PubMed PMID: 33841364; PubMed Central PMCID: PMC8024649.
Wang X, Pereira JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee TS. Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450. Metab Eng. 2021 Mar;64:41-51. doi: 10.1016/j.ymben.2021.01.004. Epub 2021 Jan 19. PubMed PMID: 33482331; PubMed Central PMCID: PMC7987753.
Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS. Engineering Saccharomyces cerevisiae for isoprenol production. Metab Eng. 2021 Mar;64:154-166. doi: 10.1016/j.ymben.2021.02.002. Epub 2021 Feb 10. PubMed PMID: 33581331.
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. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 Feb;18(2):156-164. doi: 10.1038/s41592-020-01051-w. Epub 2021 Feb 4. PubMed PMID: 33542514; PubMed Central PMCID: PMC7864804.
Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD. CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):48-61. doi: 10.1107/S2059798320015879. Epub 2021 Jan 1. PubMed PMID: 33404525; PubMed Central PMCID: PMC7787109.
Moriarty NW, Liebschner D, Tronrud DE, Adams PD. Arginine off-kilter: guanidinium is not as planar as restraints denote. Acta Crystallogr D Struct Biol. 2020 Dec 1;76(Pt 12):1159-1166. doi: 10.1107/S2059798320013534. Epub 2020 Nov 24. PubMed PMID: 33263321; PubMed Central PMCID: PMC7709202.
Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML, Joosten RP, Perrakis A, Adams PD. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure. 2020 Nov 3;28(11):1249-1258.e2. doi: 10.1016/j.str.2020.08.005. Epub 2020 Aug 27. PubMed PMID: 32857966; PubMed Central PMCID: PMC7642142.
Ge X, Thorgersen MP, Poole FL 2nd, Deutschbauer AM, Chandonia JM, Novichkov PS, Adams PD, Arkin AP, Hazen TC, Adams MWW. Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiol Resour Announc. 2020 Oct 29;9(44). doi: 10.1128/MRA.01149-20. PubMed PMID: 33122416; PubMed Central PMCID: PMC7595952.
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