Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. DNA mismatches reveal conformational penalties in protein-DNA recognition. Nature. 2020 Oct 21;. doi: 10.1038/s41586-020-2843-2. [Epub ahead of print] PubMed PMID: 33087930; NIHMSID:NIHMS1630484.
Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. Nat Plants. 2020 Sep;6(9):1158-1166. doi: 10.1038/s41477-020-00762-4. Epub 2020 Aug 31. PubMed PMID: 32868887.
Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, Afonine PV. Improvement of cryo-EM maps by density modification. Nat Methods. 2020 Sep;17(9):923-927. doi: 10.1038/s41592-020-0914-9. Epub 2020 Aug 17. PubMed PMID: 32807957; PubMed Central PMCID: PMC7484085.
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 Aug 21;. doi: 10.1016/j.str.2020.08.005. [Epub ahead of print] PubMed PMID: 32857966; NIHMSID:NIHMS1624789.
Thompson MG, Blake-Hedges JM, Pereira JH, Hangasky JA, Belcher MS, Moore WM, Barajas JF, Cruz-Morales P, Washington LJ, Haushalter RW, Eiben CB, Liu Y, Skyrud W, Benites VT, Barnum TP, Baidoo EEK, Scheller HV, Marletta MA, Shih PM, Adams PD, Keasling JD. An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Nat Commun. 2020 Jun 10;11(1):2931. doi: 10.1038/s41467-020-16815-3. PubMed PMID: 32523014; PubMed Central PMCID: PMC7286885.
Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12624-12635. doi: 10.1073/pnas.2000529117. Epub 2020 May 20. PubMed PMID: 32434915; PubMed Central PMCID: PMC7293653.
Curran SC, Pereira JH, Baluyot MJ, Lake J, Puetz H, Rosenburg DJ, Adams P, Keasling JD. Structure and Function of BorB, the Type II Thioesterase from the Borrelidin Biosynthetic Gene Cluster. Biochemistry. 2020 Apr 28;59(16):1630-1639. doi: 10.1021/acs.biochem.0c00126. Epub 2020 Apr 13. PubMed PMID: 32250597.
Park MR, Chen Y, Thompson M, Benites VT, Fong B, Petzold CJ, Baidoo EEK, Gladden JM, Adams PD, Keasling JD, Simmons BA, Singer SW. Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass. ChemSusChem. 2020 Mar 11;. doi: 10.1002/cssc.202000268. [Epub ahead of print] PubMed PMID: 32160408.
Liebschner D, Afonine PV, Moriarty NW, Adams PD. What are the current limits on determination of protonation state using neutron macromolecular crystallography?. Methods Enzymol. 2020;634:225-255. doi: 10.1016/bs.mie.2020.01.008. Epub 2020 Feb 13. PubMed PMID: 32093835; PubMed Central PMCID: PMC7571246.
Liebschner D, Afonine PV, Urzhumtsev AG, Adams PD. Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix. Methods Enzymol. 2020;634:177-199. doi: 10.1016/bs.mie.2020.01.007. Epub 2020 Feb 13. PubMed PMID: 32093832; PubMed Central PMCID: PMC7574815.
Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD. Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase. J Am Chem Soc. 2020 Jan 15;142(2):835-846. doi: 10.1021/jacs.9b09187. Epub 2020 Jan 2. PubMed PMID: 31793780.
Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix. Acta Crystallogr D Struct Biol. 2020 Jan 1;76(Pt 1):51-62. doi: 10.1107/S2059798319015134. Epub 2020 Jan 1. PubMed PMID: 31909743; PubMed Central PMCID: PMC6939439.
Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Cryo-EM map interpretation and protein model-building using iterative map segmentation. Protein Sci. 2020 Jan;29(1):87-99. doi: 10.1002/pro.3740. Epub 2019 Oct 24. PubMed PMID: 31599033; PubMed Central PMCID: PMC6933853.
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN Jr, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure. 2019 Dec 3;27(12):1745-1759. doi: 10.1016/j.str.2019.11.002. Epub 2019 Nov 25. PubMed PMID: 31780431; PubMed Central PMCID: PMC7108332.
Kang A, Mendez-Perez D, Goh EB, Baidoo EEK, Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS. Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli. Metab Eng. 2019 Dec;56:85-96. doi: 10.1016/j.ymben.2019.09.003. Epub 2019 Sep 6. PubMed PMID: 31499175.
Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry. 2019 Nov 12;58(45):4466-4479. doi: 10.1021/acs.biochem.9b00525. Epub 2019 Nov 4. PubMed PMID: 31659895; NIHMSID:NIHMS1627189.
Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ. Automated "Cells-To-Peptides" Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes. J Proteome Res. 2019 Oct 4;18(10):3752-3761. doi: 10.1021/acs.jproteome.9b00455. Epub 2019 Aug 30. PubMed PMID: 31436101.
Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol. 2019 Oct 1;75(Pt 10):861-877. doi: 10.1107/S2059798319011471. Epub 2019 Oct 2. PubMed PMID: 31588918; PubMed Central PMCID: PMC6778852.
Kim DN, Moriarty NW, Kirmizialtin S, Afonine PV, Poon B, Sobolev OV, Adams PD, Sanbonmatsu K. Cryo_fit: Democratization of flexible fitting for cryo-EM. J Struct Biol. 2019 Oct 1;208(1):1-6. doi: 10.1016/j.jsb.2019.05.012. Epub 2019 Jul 3. PubMed PMID: 31279069; PubMed Central PMCID: PMC7112765.
Barajas JF, McAndrew RP, Thompson MG, Backman TWH, Pang B, de Rond T, Pereira JH, Benites VT, Martín HG, Baidoo EEK, Hillson NJ, Adams PD, Keasling JD. Structural insights into dehydratase substrate selection for the borrelidin and fluvirucin polyketide synthases. J Ind Microbiol Biotechnol. 2019 Aug;46(8):1225-1235. doi: 10.1007/s10295-019-02189-z. Epub 2019 May 21. PubMed PMID: 31115703; PubMed Central PMCID: PMC6697708.
Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW. Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids. Biotechnol Bioeng. 2019 Aug;116(8):1909-1922. doi: 10.1002/bit.26995. Epub 2019 Apr 29. PubMed PMID: 30982958.
Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD. Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism. mBio. 2019 May 7;10(3). doi: 10.1128/mBio.02577-18. PubMed PMID: 31064836; PubMed Central PMCID: PMC6509195.
Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):451-454. doi: 10.1107/S2059798319004522. Epub 2019 Apr 8. PubMed PMID: 30988261; PubMed Central PMCID: PMC6465986.
Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ. A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS One. 2019;14(2):e0211582. doi: 10.1371/journal.pone.0211582. eCollection 2019. PubMed PMID: 30763335; PubMed Central PMCID: PMC6375547.
Moriarty NW, Adams PD. Iron-sulfur clusters have no right angles. Acta Crystallogr D Struct Biol. 2019 Jan 1;75(Pt 1):16-20. doi: 10.1107/S205979831801519X. Epub 2019 Jan 4. PubMed PMID: 30644841; PubMed Central PMCID: PMC6333285.
Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW. Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle. Environ Microbiol. 2019 Jan;21(1):152-163. doi: 10.1111/1462-2920.14435. Epub 2018 Nov 21. PubMed PMID: 30289197.
Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nat Methods. 2018 Nov;15(11):905-908. doi: 10.1038/s41592-018-0173-1. Epub 2018 Oct 30. PubMed PMID: 30377346; PubMed Central PMCID: PMC6214191.
Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J Struct Biol. 2018 Nov;204(2):338-343. doi: 10.1016/j.jsb.2018.07.016. Epub 2018 Jul 29. PubMed PMID: 30063987; PubMed Central PMCID: PMC6163059.
Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun. 2018 Oct 30;9(1):4596. doi: 10.1038/s41467-018-07111-2. PubMed PMID: 30375402; PubMed Central PMCID: PMC6207686.
Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS. Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli. Biotechnol Biofuels. 2018;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018. PubMed PMID: 30377444; PubMed Central PMCID: PMC6195743.
Kryshtafovych A, Adams PD, Lawson CL, Chiu W. Evaluation system and web infrastructure for the second cryo-EM model challenge. J Struct Biol. 2018 Oct;204(1):96-108. doi: 10.1016/j.jsb.2018.07.006. Epub 2018 Jul 12. PubMed PMID: 30017700; PubMed Central PMCID: PMC6205695.
Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W. Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. Data Brief. 2018 Oct;20:1629-1638. doi: 10.1016/j.dib.2018.08.214. eCollection 2018 Oct. PubMed PMID: 30263915; PubMed Central PMCID: PMC6157618.
Deng K, Zeng J, Cheng G, Gao J, Sale KL, Simmons BA, Singh AK, Adams PD, Northen TR. Rapid characterization of the activities of lignin-modifying enzymes based on nanostructure-initiator mass spectrometry (NIMS). Biotechnol Biofuels. 2018;11:266. doi: 10.1186/s13068-018-1261-2. eCollection 2018. PubMed PMID: 30275906; PubMed Central PMCID: PMC6158898.
Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nat Commun. 2018 Sep 6;9(1):3617. doi: 10.1038/s41467-018-05857-3. PubMed PMID: 30190458; PubMed Central PMCID: PMC6127294.
Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol. 2018 Sep 1;74(Pt 9):814-840. doi: 10.1107/S2059798318009324. Epub 2018 Sep 3. PubMed PMID: 30198894; PubMed Central PMCID: PMC6130467.
Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Crystallogr D Struct Biol. 2018 Aug 1;74(Pt 8):800-813. doi: 10.1107/S2059798318004588. Epub 2018 Jul 24. Review. PubMed PMID: 30082516; PubMed Central PMCID: PMC6079631.
Afonine PV, Adams PD, Urzhumtsev A. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. Acta Crystallogr D Struct Biol. 2018 Jul 1;74(Pt 7):621-631. doi: 10.1107/S2059798318005764. Epub 2018 Jun 8. PubMed PMID: 29968672; PubMed Central PMCID: PMC6038382.
Terwilliger TC, Sobolev OV, Afonine PV, Adams PD. Automated map sharpening by maximization of detail and connectivity. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):545-559. doi: 10.1107/S2059798318004655. Epub 2018 May 18. PubMed PMID: 29872005; PubMed Central PMCID: PMC6096490.
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi: 10.1107/S2059798318006551. Epub 2018 May 30. PubMed PMID: 29872004; PubMed Central PMCID: PMC6096492.
Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7. PubMed PMID: 29278415.
Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE. Employing a biochemical protecting group for a sustainable indigo dyeing strategy. Nat Chem Biol. 2018 Mar;14(3):256-261. doi: 10.1038/nchembio.2552. Epub 2018 Jan 8. PubMed PMID: 29309053; PubMed Central PMCID: PMC5866135.
Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd JJ, Poon BK, Adams PD. Interactive comparison and remediation of collections of macromolecular structures. Protein Sci. 2018 Jan;27(1):182-194. doi: 10.1002/pro.3296. Epub 2017 Nov 11. PubMed PMID: 28901593; PubMed Central PMCID: PMC5734393.
Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol. 2018 Jan;3(1):99-107. doi: 10.1038/s41564-017-0052-z. Epub 2017 Nov 6. PubMed PMID: 29109478; PubMed Central PMCID: PMC6794216.
Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018 Jan;27(1):293-315. doi: 10.1002/pro.3330. Epub 2017 Nov 27. PubMed PMID: 29067766; PubMed Central PMCID: PMC5734394.
Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, Gladden JM. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. PLoS One. 2017;12(12):e0189604. doi: 10.1371/journal.pone.0189604. eCollection 2017. PubMed PMID: 29281693; PubMed Central PMCID: PMC5744941.
Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization. ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8. PubMed PMID: 28826210.
Pereira JH, McAndrew RP, Tomaleri GP, Adams PD. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. J Appl Crystallogr. 2017 Oct 1;50(Pt 5):1352-1358. doi: 10.1107/S1600576717011347. eCollection 2017 Oct 1. PubMed PMID: 29021733; PubMed Central PMCID: PMC5627680.
Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E. The cryo-electron microscopy structure of human transcription factor IIH. Nature. 2017 Sep 21;549(7672):414-417. doi: 10.1038/nature23903. Epub 2017 Sep 13. PubMed PMID: 28902838; PubMed Central PMCID: PMC5844561.
Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnol Bioeng. 2017 Aug;114(8):1703-1712. doi: 10.1002/bit.26296. Epub 2017 May 18. PubMed PMID: 28369701.
McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD. Reply to Kiser: Dioxygen binding in NOV1 crystal structures. Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):E6029-E6030. doi: 10.1073/pnas.1708124114. Epub 2017 Jul 5. PubMed PMID: 28679635; PubMed Central PMCID: PMC5544338.
What would you like to do?