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    Adams, Paul

    TitleScientific Division Director
    SchoolLawrence Berkeley National Lab
    DepartmentMolecular Biophys & Integ Bio
    Address1 Cyclotron Road
    Berkeley CA 94720
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams P, Dueber JE. Employing a biochemical protecting group for a sustainable indigo dyeing strategy. Nat Chem Biol. 2018 Jan 08. PMID: 29309053.
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      2. Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams P, 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. PMID: 29281693.
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      3. Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams P, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Towards industrial production of isoprenoids in Escherichia coli: lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng. 2017 Dec 26. PMID: 29278415.
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      4. 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, Snoeyink J, Adams P, 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. PMID: 29067766.
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      5. 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 P, 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. PMID: 29109478.
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      6. Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd J, Poon BK, Adams P. Interactive Comparison and Remediation of Collections of Macromolecular Structures. Protein Sci. 2017 Sep 13. PMID: 28901593.
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      7. Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams P, Nogales E. The cryo-electron microscopy structure of human transcription factor IIH. Nature. 2017 Sep 21; 549(7672):414-417. PMID: 28902838.
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      8. 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 P, 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 Sep 08. PMID: 28826210.
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      9. Pereira JH, McAndrew RP, Tomaleri GP, Adams P. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. J Appl Crystallogr. 2017 Oct 01; 50(Pt 5):1352-1358. PMID: 29021733.
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      10. Pereira JH, McAndrew RP, Sergeeva OA, Ralston CY, King JA, Adams P. Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy. Sci Rep. 2017 Jun 16; 7(1):3673. PMID: 28623285.
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      11. Welner DH, Shin D, Tomaleri GP, DeGiovanni AM, Tsai AY, Tran HM, Hansen SF, Green DT, Scheller HV, Adams P. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. PLoS One. 2017; 12(6):e0177591. PMID: 28598995.
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      12. Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams P, Petzold CJ, Keasling JD, Lee TS. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnol Bioeng. 2017 Aug; 114(8):1703-1712. PMID: 28369701.
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      13. Kohler AC, Mills MJ, Adams P, Simmons BA, Sale KL. Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proc Natl Acad Sci U S A. 2017 Apr 03. PMID: 28373573.
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      14. Welner DH, Tsai AY, DeGiovanni AM, Scheller HV, Adams P. X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa. Acta Crystallogr F Struct Biol Commun. 2017 Apr 01; 73(Pt 4):241-245. PMID: 28368284.
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      15. Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams P, King JA, Schmid MF, Chiu W. Accurate model annotation of a near-atomic resolution cryo-EM map. Proc Natl Acad Sci U S A. 2017 Mar 21; 114(12):3103-3108. PMID: 28270620.
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      16. Moriarty NW, Draizen EJ, Adams P. An editor for the generation and customization of geometry restraints. Acta Crystallogr D Struct Biol. 2017 Feb 01; 73(Pt 2):123-130. PMID: 28177308.
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      17. Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams P. Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallogr D Struct Biol. 2017 Feb 01; 73(Pt 2):148-157. PMID: 28177311.
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      18. Heinemann J, Deng K, Shih SC, Gao J, Adams P, Singh AK, Northen TR. On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab Chip. 2017 01 17; 17(2):323-331. PMID: 27957569.
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      19. McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams P. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proc Natl Acad Sci U S A. 2016 Dec 13; 113(50):14324-14329. PMID: 27911781.
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      20. Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams P, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature. 2016 12 15; 540(7633):453-457. PMID: 27871088.
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      21. Yuzawa S, Deng K, Wang G, Baidoo EE, Northen TR, Adams P, Katz L, Keasling JD. Comprehensive in Vitro Analysis of Acyltransferase Domain Exchanges in Modular Polyketide Synthases and Its Application for Short-Chain Ketone Production. ACS Synth Biol. 2017 01 20; 6(1):139-147. PMID: 27548700.
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      22. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams P. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Crystallogr D Struct Biol. 2016 Sep 01; 72(Pt 9):1073-1075. PMID: 27599739.
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      23. Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams P, Warren GL. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallogr D Struct Biol. 2016 Sep; 72(Pt 9):1062-72. PMID: 27599738.
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      24. Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams P, Northen TR, Simmons BA, Singer SW. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis. MBio. 2016 Aug 23; 7(4). PMID: 27555310; PMCID: PMC4999548.
      25. Sauter NK, Echols N, Adams P, Zwart PH, Kern J, Brewster AS, Koroidov S, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Yano J, Yachandra VK. No observable conformational changes in PSII. Nature. 2016 05 19; 533(7603):E1-2. PMID: 27193689.
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      26. Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams P, Keasling JD, Palsson BO, Lee TS. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Syst. 2016 May 25; 2(5):335-46. PMID: 27211860; PMCID: PMC4882250 [Available on 05/25/17].
      27. Adams P, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure. 2016 Apr 05; 24(4):502-508. PMID: 27050687.
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      28. Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams P. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin ß-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem. 2016 May 06; 291(19):10228-38. PMID: 26940872; PMCID: PMC4858972.
      29. Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams P. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. Acta Crystallogr D Struct Biol. 2016 Mar; 72(Pt 3):346-58. PMID: 26960122; PMCID: PMC4784666.
      30. Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams P. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. Acta Crystallogr D Struct Biol. 2016 Mar; 72(Pt 3):359-74. PMID: 26960123; PMCID: PMC4784667.
      31. Gach PC, Shih SC, Sustarich J, Keasling JD, Hillson NJ, Adams P, Singh AK. A Droplet Microfluidic Platform for Automating Genetic Engineering. ACS Synth Biol. 2016 May 20; 5(5):426-33. PMID: 26830031.
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      32. Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EE, Lee TS, Adams P, Keasling JD, Loqué D. Exploiting the Substrate Promiscuity of Hydroxycinnamoyl-CoA:Shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Plant Cell Physiol. 2016 Mar; 57(3):568-79. PMID: 26858288; PMCID: PMC4790474.
      33. Morris KM, Henderson R, Suresh Kumar TK, Heyes CD, Adams P. Intrinsic GTP hydrolysis is observed for a switch 1 variant of Cdc42 in the presence of a specific GTPase inhibitor. Small GTPases. 2016; 7(1):1-11. PMID: 26828437; PMCID: PMC4905262 [Available on 02/01/17].
      34. Moriarty NW, Tronrud DE, Adams P, Karplus PA. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. Acta Crystallogr D Struct Biol. 2016 Jan; 72(Pt 1):176-9. PMID: 26894545; PMCID: PMC4756615.
      35. Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams P, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. Biotechnol Biofuels. 2015; 8:220. PMID: 26697109.
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      36. Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams P, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of ß-Aryl Ether Bonds in Lignin. J Biol Chem. 2016 Mar 04; 291(10):5234-46. PMID: 26637355; PMCID: PMC4777856.
      37. Schwessinger B, Li X, Ellinghaus TL, Chan LJ, Wei T, Joe A, Thomas N, Pruitt R, Adams P, Chern MS, Petzold CJ, Liu CC, Ronald PC. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integr Biol (Camb). 2016 Apr 18; 8(4):542-5. PMID: 26611838.
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      38. Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams P, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Front Bioeng Biotechnol. 2015; 3:165. PMID: 26579511; PMCID: PMC4621489.
      39. Deng K, Guenther JM, Gao J, Bowen BP, Tran H, Reyes-Ortiz V, Cheng X, Sathitsuksanoh N, Heins R, Takasuka TE, Bergeman LF, Geertz-Hansen H, Deutsch S, Loqué D, Sale KL, Simmons BA, Adams P, Singh AK, Fox BG, Northen TR. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Front Bioeng Biotechnol. 2015; 3:153. PMID: 26528471; PMCID: PMC4603251.
      40. Sun L, Singh S, Joo M, Vega-Sanchez M, Ronald P, Simmons BA, Adams P, Auer M. Non-invasive imaging of cellulose microfibril orientation within plant cell walls by polarized Raman microspectroscopy. Biotechnol Bioeng. 2016 Jan; 113(1):82-90. PMID: 26137889.
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      41. Petzold CJ, Chan LJ, Nhan M, Adams P. Analytics for Metabolic Engineering. Front Bioeng Biotechnol. 2015; 3:135. PMID: 26442249; PMCID: PMC4561385.
      42. Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams P, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat Methods. 2015 Oct; 12(10):943-6. PMID: 26280328; PMCID: PMC4589481.
      43. Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams P, Urzhumtsev A, Fraser JS. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1657-67. PMID: 26249347; PMCID: PMC4528799.
      44. Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams P. From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallogr D Biol Crystallogr. 2015 Aug; 71(Pt 8):1668-83. PMID: 26249348; PMCID: PMC4528800.
      45. Sobolev OV, Afonine PV, Adams P, Urzhumtsev A. Programming new geometry restraints: parallelity of atomic groups. J Appl Crystallogr. 2015 Aug 01; 48(Pt 4):1130-1141. PMID: 26306091.
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      46. Shih SC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams P, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. ACS Synth Biol. 2015 Oct 16; 4(10):1151-64. PMID: 26075958.
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      47. George KW, Thompson MG, Kang A, Baidoo E, Wang G, Chan LJ, Adams P, Petzold CJ, Keasling JD, Lee TS. Metabolic engineering for the high-yield production of isoprenoid-based C5 alcohols in E. coli. Sci Rep. 2015 Jun 08; 5:11128. PMID: 26052683; PMCID: PMC4459108.
      48. Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams P, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC. Natural bacterial communities serve as quantitative geochemical biosensors. MBio. 2015 May 12; 6(3):e00326-15. PMID: 25968645; PMCID: PMC4436078.
      49. Morshed N, Echols N, Adams P. Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2015 May; 71(Pt 5):1147-58. PMID: 25945580; PMCID: PMC4427199.
      50. González Fernández-Niño SM, Smith-Moritz AM, Chan LJ, Adams P, Heazlewood JL, Petzold CJ. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front Bioeng Biotechnol. 2015; 3:44. PMID: 25883932; PMCID: PMC4381839.
      51. Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJ, Adams P, Petzold CJ, Pauly M, Willats WG, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. Plant Cell. 2015 Apr; 27(4):1218-27. PMID: 25804536; PMCID: PMC4558686.
      52. Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams P. FEM: feature-enhanced map. Acta Crystallogr D Biol Crystallogr. 2015 Mar; 71(Pt 3):646-66. PMID: 25760612; PMCID: PMC4356370.
      53. Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams P, Eisenberg DS, Sauter NK. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Crystallogr D Biol Crystallogr. 2015 Feb; 71(Pt 2):357-66. PMID: 25664747; PMCID: PMC4321489.
      54. Shih SC, Gach PC, Sustarich J, Simmons BA, Adams P, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab Chip. 2015 Jan 07; 15(1):225-36. PMID: 25354549.
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      55. Alonso-Gutierrez J, Kim EM, Batth TS, Cho N, Hu Q, Chan LJ, Petzold CJ, Hillson NJ, Adams P, Keasling JD, Garcia Martin H, Lee TS. Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. Metab Eng. 2015 Mar; 28:123-33. PMID: 25554074.
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      56. Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams P, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods. 2015 Feb; 12(2):127-30. PMID: 25532136; PMCID: PMC4312553.
      57. Wall ME, Van Benschoten AH, Sauter NK, Adams P, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17887-92. PMID: 25453071; PMCID: PMC4273327.
      58. Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams P. Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallogr D Biol Crystallogr. 2014 Dec 01; 70(Pt 12):3299-309. PMID: 25478847; PMCID: PMC4257623.
      59. McAndrew R, Pruitt RN, Kamita SG, Pereira JH, Majumdar D, Hammock BD, Adams P, Ronald PC. Structure of the OsSERK2 leucine-rich repeat extracellular domain. Acta Crystallogr D Biol Crystallogr. 2014 Nov; 70(Pt 11):3080-6. PMID: 25372696; PMCID: PMC4220978.
      60. Poust S, Yoon I, Adams P, Katz L, Petzold CJ, Keasling JD. Understanding the role of histidine in the GHSxG acyltransferase active site motif: evidence for histidine stabilization of the malonyl-enzyme intermediate. PLoS One. 2014; 9(10):e109421. PMID: 25286165; PMCID: PMC4186864.
      61. Rhee M, Light YK, Yilmaz S, Adams P, Saxena D, Meagher RJ, Singh AK. Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Lab Chip. 2014 Dec 07; 14(23):4533-9. PMID: 25270338; PMCID: PMC4213212.
      62. Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams P. Metrics for comparison of crystallographic maps. Acta Crystallogr D Biol Crystallogr. 2014 Oct; 70(Pt 10):2593-606. PMID: 25286844; PMCID: PMC4188004.
      63. Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams P, Petzold CJ, Katz L, Keasling JD. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metab Eng. 2014 Nov; 26:111-118. PMID: 25250846.
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      64. Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams P, Petzold CJ, Keasling JD. In vitro analysis of carboxyacyl substrate tolerance in the loading and first extension modules of borrelidin polyketide synthase. Biochemistry. 2014 Sep 30; 53(38):5975-7. PMID: 25188840.
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      65. Batth TS, Singh P, Ramakrishnan VR, Sousa MML, Chan LJG, Tran HM, Luning EG, Pan EHY, Vuu KM, Keasling JD, Adams P, Petzold CJ. A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metab Eng. 2014 Nov; 26:48-56. PMID: 25205128.
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      66. Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams P, Chiu W. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun. 2014 Sep 04; 5:4808. PMID: 25185801; PMCID: PMC4155512.
      67. Ghosh A, Nilmeier J, Weaver D, Adams P, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. PLoS Comput Biol. 2014 Sep; 10(9):e1003827. PMID: 25188426; PMCID: PMC4154649.
      68. Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams P, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV. Identification of a sphingolipid a-glucuronosyltransferase that is essential for pollen function in Arabidopsis. Plant Cell. 2014 Aug; 26(8):3314-25. PMID: 25122154; PMCID: PMC4371831.
      69. Pereira JH, Petchprayoon C, Hoepker AC, Moriarty NW, Fink SJ, Cecere G, Paterson I, Adams P, Marriott G. Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues. ChemMedChem. 2014 Oct; 9(10):2286-93. PMID: 25047814; PMCID: PMC4213943.
      70. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams P, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 ß-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19; 9(9):2082-91. PMID: 24984213; PMCID: PMC4168791.
      71. Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glöckner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams P, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun. 2014 Jul 09; 5:4371. PMID: 25006873; PMCID: PMC4151126.
      72. Lao J, Oikawa A, Bromley JR, McInerney P, Suttangkakul A, Smith-Moritz AM, Plahar H, Chiu TY, González Fernández-Niño SM, Ebert B, Yang F, Christiansen KM, Hansen SF, Stonebloom S, Adams P, Ronald PC, Hillson NJ, Hadi MZ, Vega-Sánchez ME, Loqué D, Scheller HV, Heazlewood JL. The plant glycosyltransferase clone collection for functional genomics. Plant J. 2014 Aug; 79(3):517-29. PMID: 24905498.
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      73. Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams P, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One. 2014; 9(7):e101115. PMID: 24983352; PMCID: PMC4077768.
      74. Dougherty MJ, Tran HM, Stavila V, Knierim B, George A, Auer M, Adams P, Hadi MZ. Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size. PLoS One. 2014; 9(6):e100836. PMID: 24971883; PMCID: PMC4074075.
      75. Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams P, Keasling JD. Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. Structure. 2014 Jul 08; 22(7):1028-36. PMID: 24954619.
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      76. Moriarty NW, Tronrud DE, Adams P, Karplus PA. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. FEBS J. 2014 Sep; 281(18):4061-71. PMID: 24890778; PMCID: PMC4169323.
      77. Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams P, Singh AK, Fox BG, Northen TR. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). ACS Chem Biol. 2014 Jul 18; 9(7):1470-9. PMID: 24819174.
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      78. George KW, Chen A, Jain A, Batth TS, Baidoo EE, Wang G, Adams P, Petzold CJ, Keasling JD, Lee TS. Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnol Bioeng. 2014 Aug; 111(8):1648-58. PMID: 24615242.
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      79. Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams P. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallogr D Biol Crystallogr. 2014 May; 70(Pt 5):1346-56. PMID: 24816103; PMCID: PMC4014122.
      80. Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams P. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 2014 Apr; 70(Pt 4):1104-14. PMID: 24699654; PMCID: PMC3975891.
      81. Hattne J, Echols N, Tran R, Kern J, Gildea RJ, Brewster AS, Alonso-Mori R, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Lampe A, Han G, Gul S, DiFiore D, Milathianaki D, Fry AR, Miahnahri A, White WE, Schafer DW, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Glatzel P, Zwart PH, Grosse-Kunstleve RW, Bogan MJ, Messerschmidt M, Williams GJ, Boutet S, Messinger J, Zouni A, Yano J, Bergmann U, Yachandra VK, Adams P, Sauter NK. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nat Methods. 2014 May; 11(5):545-8. PMID: 24633409; PMCID: PMC4008696.
      82. Wall ME, Adams P, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure. 2014 Feb 04; 22(2):182-4. PMID: 24507780; PMCID: PMC4070675.
      83. Parsons HT, Weinberg CS, Macdonald LJ, Adams P, Petzold CJ, Strabala TJ, Wagner A, Heazlewood JL. Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis. PLoS One. 2013; 8(12):e84669. PMID: 24416096; PMCID: PMC3887118.
      84. Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams P. Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr. 2014 Jan; 70(Pt 1):144-54. PMID: 24419387; PMCID: PMC3919266.
      85. Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams P. Ligand placement based on prior structures: the guided ligand-replacement method. Acta Crystallogr D Biol Crystallogr. 2014 Jan; 70(Pt 1):134-43. PMID: 24419386; PMCID: PMC3919265.
      86. Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams P, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal ß-glucosidase production. Front Microbiol. 2013; 4:365. PMID: 24367356; PMCID: PMC3854461.
      87. Ito J, Herter T, Baidoo EE, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams P, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Anal Biochem. 2014 Mar 01; 448:14-22. PMID: 24299991.
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      88. Chen Z, Pereira JH, Liu H, Tran HM, Hsu NS, Dibble D, Singh S, Adams P, Sapra R, Hadi MZ, Simmons BA, Sale KL. Improved activity of a thermophilic cellulase, Cel5A, from Thermotoga maritima on ionic liquid pretreated switchgrass. PLoS One. 2013; 8(11):e79725. PMID: 24244549; PMCID: PMC3828181.
      89. Javidpour P, Pereira JH, Goh EB, McAndrew RP, Ma SM, Friedland GD, Keasling JD, Chhabra SR, Adams P, Beller HR. Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions. Appl Environ Microbiol. 2014 Jan; 80(2):497-505. PMID: 24212572; PMCID: PMC3911115.
      90. Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams P, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol. 2013 Nov; 31(11):1039-46. PMID: 24142050.
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      91. Terwilliger TC, Read RJ, Adams P, Brunger AT, Afonine PV, Hung LW. Model morphing and sequence assignment after molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 69(Pt 11):2244-50. PMID: 24189236; PMCID: PMC3817698.
      92. Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams P, Read RJ. Phaser.MRage: automated molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013 Nov; 69(Pt 11):2276-86. PMID: 24189240; PMCID: PMC3817702.
      93. DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams P, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nat Methods. 2013 Nov; 10(11):1102-4. PMID: 24076763; PMCID: PMC4116791.
      94. Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams P, Terwilliger TC, Nettles KW. Improved crystallographic structures using extensive combinatorial refinement. Structure. 2013 Nov 05; 21(11):1923-30. PMID: 24076406; PMCID: PMC4070946.
      95. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams P, King JA, Jiang W, Chiu W. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc Natl Acad Sci U S A. 2013 Jul 23; 110(30):12301-6. PMID: 23840063; PMCID: PMC3725109.
      96. Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams P, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol Biofuels. 2013 Jul 03; 6(1):93. PMID: 23819686; PMCID: PMC3716932.
      97. Urzhumtsev A, Afonine PV, Adams P. TLS from fundamentals to practice. Crystallogr Rev. 2013 Jul 01; 19(4):230-270. PMID: 25249713.
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      98. Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams P, Singh AK. A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres. Chem Commun (Camb). 2013 Jun 18; 49(48):5441-3. PMID: 23536035.
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      99. Alonso-Gutierrez J, Chan R, Batth TS, Adams P, Keasling JD, Petzold CJ, Lee TS. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metab Eng. 2013 Sep; 19:33-41. PMID: 23727191.
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      100. Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams P, Singh AK. Droplet-based microfluidic platform for heterogeneous enzymatic assays. Lab Chip. 2013 May 07; 13(9):1817-22. PMID: 23507976.
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      101. McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams P. From soil to structure, a novel dimeric ß-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem. 2013 May 24; 288(21):14985-92. PMID: 23580647; PMCID: PMC3663519.
      102. Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams P, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci. 2013; 4:83. PMID: 23596448; PMCID: PMC3622038.
      103. Afonine PV, Grosse-Kunstleve RW, Adams P, Urzhumtsev A. Bulk-solvent and overall scaling revisited: faster calculations, improved results. Acta Crystallogr D Biol Crystallogr. 2013 Apr; 69(Pt 4):625-34. PMID: 23519671; PMCID: PMC3606040.
      104. Adams P, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu Rev Biophys. 2013; 42:265-87. PMID: 23451892.
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      105. Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glöckner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams P, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J. Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science. 2013 Apr 26; 340(6131):491-5. PMID: 23413188; PMCID: PMC3732582.
      106. Varanasi P, Singh P, Auer M, Adams P, Simmons BA, Singh S. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels. 2013 Jan 28; 6(1):14. PMID: 23356589; PMCID: PMC3579681.
      107. Read RJ, Adams P, McCoy AJ. Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Crystallogr D Biol Crystallogr. 2013 Feb; 69(Pt 2):176-83. PMID: 23385454; PMCID: PMC3565438.
      108. Burnley BT, Afonine PV, Adams P, Gros P. Modelling dynamics in protein crystal structures by ensemble refinement. Elife. 2012 Dec 18; 1:e00311. PMID: 23251785; PMCID: PMC3524795.
      109. Alonso-Mori R, Kern J, Gildea RJ, Sokaras D, Weng TC, Lassalle-Kaiser B, Tran R, Hattne J, Laksmono H, Hellmich J, Glöckner C, Echols N, Sierra RG, Schafer DW, Sellberg J, Kenney C, Herbst R, Pines J, Hart P, Herrmann S, Grosse-Kunstleve RW, Latimer MJ, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Zwart PH, White WE, Adams P, Bogan MJ, Boutet S, Williams GJ, Zouni A, Messinger J, Glatzel P, Sauter NK, Yachandra VK, Yano J, Bergmann U. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proc Natl Acad Sci U S A. 2012 Nov 20; 109(47):19103-7. PMID: 23129631; PMCID: PMC3511075.
      110. Sierra RG, Laksmono H, Kern J, Tran R, Hattne J, Alonso-Mori R, Lassalle-Kaiser B, Glöckner C, Hellmich J, Schafer DW, Echols N, Gildea RJ, Grosse-Kunstleve RW, Sellberg J, McQueen TA, Fry AR, Messerschmidt MM, Miahnahri A, Seibert MM, Hampton CY, Starodub D, Loh ND, Sokaras D, Weng TC, Zwart PH, Glatzel P, Milathianaki D, White WE, Adams P, Williams GJ, Boutet S, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK, Bogan MJ. Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallogr D Biol Crystallogr. 2012 Nov; 68(Pt 11):1584-7. PMID: 23090408; PMCID: PMC3478121.
      111. Zhang F, Ouellet M, Batth TS, Adams P, Petzold CJ, Mukhopadhyay A, Keasling JD. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng. 2012 Nov; 14(6):653-60. PMID: 23026122.
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      112. Pereira JH, Goh EB, Keasling JD, Beller HR, Adams P. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Crystallogr D Biol Crystallogr. 2012 Oct; 68(Pt 10):1320-8. PMID: 22993086; PMCID: PMC3447401.
      113. Varanasi P, Singh P, Arora R, Adams P, Auer M, Simmons BA, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol. 2012 Dec; 126:156-61. PMID: 23073103.
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      114. McClendon SD, Batth T, Petzold CJ, Adams P, Simmons BA, Singer SW. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnol Biofuels. 2012 Jul 28; 5(1):54. PMID: 22839529; PMCID: PMC3507748.
      115. Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams P, Hadi MZ. Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol. 2012 Jul 03; 12:38. PMID: 22759983; PMCID: PMC3477009.
      116. Terwilliger TC, Read RJ, Adams P, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Crystallogr D Biol Crystallogr. 2012 Jul; 68(Pt 7):861-70. PMID: 22751672; PMCID: PMC3388814.
      117. McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams P, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microb Cell Fact. 2012 Jun 13; 11:79. PMID: 22694848; PMCID: PMC3460784.
      118. Brunger AT, Adams P, Fromme P, Fromme R, Levitt M, Schröder GF. Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure. 2012 Jun 06; 20(6):957-66. PMID: 22681901; PMCID: PMC3380535.
      119. Kern J, Alonso-Mori R, Hellmich J, Tran R, Hattne J, Laksmono H, Glöckner C, Echols N, Sierra RG, Sellberg J, Lassalle-Kaiser B, Gildea RJ, Glatzel P, Grosse-Kunstleve RW, Latimer MJ, McQueen TA, DiFiore D, Fry AR, Messerschmidt M, Miahnahri A, Schafer DW, Seibert MM, Sokaras D, Weng TC, Zwart PH, White WE, Adams P, Bogan MJ, Boutet S, Williams GJ, Messinger J, Sauter NK, Zouni A, Bergmann U, Yano J, Yachandra VK. Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proc Natl Acad Sci U S A. 2012 Jun 19; 109(25):9721-6. PMID: 22665786; PMCID: PMC3382516.
      120. Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams P, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. J Biol Chem. 2012 Jul 20; 287(30):25335-43. PMID: 22645145; PMCID: PMC3408205.
      121. Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams P. Automatic Fortran to C++ conversion with FABLE. Source Code Biol Med. 2012 May 28; 7(1):5. PMID: 22640868; PMCID: PMC3448510.
      122. Echols N, Grosse-Kunstleve RW, Afonine PV, Bunkóczi G, Chen VB, Headd JJ, McCoy AJ, Moriarty NW, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Adams P. Graphical tools for macromolecular crystallography in PHENIX. J Appl Crystallogr. 2012 Jun 01; 45(Pt 3):581-586. PMID: 22675231.
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      123. Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams P. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J Struct Funct Genomics. 2012 Jun; 13(2):57-62. PMID: 22527514; PMCID: PMC3588887.
      124. Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams P, Petzold CJ. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics. 2012 Apr; 12(8):1289-99. PMID: 22577029.
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      125. Deng K, George KW, Reindl W, Keasling JD, Adams P, Lee TS, Singh AK, Northen TR. Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme. Rapid Commun Mass Spectrom. 2012 Mar 30; 26(6):611-5. PMID: 22328213.
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      126. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams P. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr. 2012 Apr; 68(Pt 4):352-67. PMID: 22505256; PMCID: PMC3322595.
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      128. Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams P, Levitt M, Schröder GF. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum. Acta Crystallogr D Biol Crystallogr. 2012 Apr; 68(Pt 4):391-403. PMID: 22505259; PMCID: PMC3322598.
      129. Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams P, Grosse-Kunstleve RW, Afonine PV, Echols N. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J Struct Funct Genomics. 2012 Jun; 13(2):81-90. PMID: 22418934; PMCID: PMC3375004.
      130. Groff D, Benke PI, Batth TS, Bokinsky G, Petzold CJ, Adams P, Keasling JD. Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars. Appl Environ Microbiol. 2012 Apr; 78(7):2221-9. PMID: 22286982; PMCID: PMC3302627.
      131. Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams P. Mechanism of nucleotide sensing in group II chaperonins. EMBO J. 2012 Feb 01; 31(3):731-40. PMID: 22193720; PMCID: PMC3273386.
      132. McAndrew RP, Peralta-Yahya PP, DeGiovanni A, Pereira JH, Hadi MZ, Keasling JD, Adams P. Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure. 2011 Dec 07; 19(12):1876-84. PMID: 22153510.
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      133. Perera PN, Schmidt M, Chiang VL, Schuck PJ, Adams P. Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Anal Bioanal Chem. 2012 Jan; 402(2):983-7. PMID: 22071606.
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      134. Gildea RJ, Bourhis LJ, Dolomanov OV, Grosse-Kunstleve RW, Puschmann H, Adams P, Howard JA. iotbx.cif: a comprehensive CIF toolbox. J Appl Crystallogr. 2011 Dec 01; 44(Pt 6):1259-1263. PMID: 22199401.
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      135. Read RJ, Adams P, Arendall WB, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. A new generation of crystallographic validation tools for the protein data bank. Structure. 2011 Oct 12; 19(10):1395-412. PMID: 22000512; PMCID: PMC3195755.
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      137. Perera PN, Schmidt M, Schuck PJ, Adams P. Blind image analysis for the compositional and structural characterization of plant cell walls. Anal Chim Acta. 2011 Sep 30; 702(2):172-7. PMID: 21839194.
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      138. Chandrashekar R, Salem O, Krizova H, McFeeters R, Adams P. A switch I mutant of Cdc42 exhibits less conformational freedom. Biochemistry. 2011 Jul 19; 50(28):6196-207. PMID: 21667996; PMCID: PMC3134622.
      139. Gabanyi MJ, Adams P, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics. 2011 Jul; 12(2):45-54. PMID: 21472436; PMCID: PMC3123456.
      140. Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams P. Exact direct-space asymmetric units for the 230 crystallographic space groups. Acta Crystallogr A. 2011 May; 67(Pt 3):269-75. PMID: 21487185; PMCID: PMC3082335.
      141. Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams P, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metab Eng. 2011 Mar; 13(2):194-203. PMID: 21215324.
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      142. Schmidt M, Perera P, Schwartzberg AM, Adams P, Schuck PJ. Label-free in situ imaging of lignification in plant cell walls. J Vis Exp. 2010 Nov 01; (45). PMID: 21085100; PMCID: PMC3157855.
      143. Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons BA, Adams P, Singh AK. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion. Anal Chem. 2010 Nov 15; 82(22):9513-20. PMID: 20964411.
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      144. Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams P. Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr. 2010 Nov; 66(Pt 11):1153-63. PMID: 21041930; PMCID: PMC2967420.
      145. Bruning JB, Parent AA, Gil G, Zhao M, Nowak J, Pace MC, Smith CL, Afonine PV, Adams P, Katzenellenbogen JA, Nettles KW. Coupling of receptor conformation and ligand orientation determine graded activity. Nat Chem Biol. 2010 Nov; 6(11):837-43. PMID: 20924370; PMCID: PMC2974172.
      146. Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams P, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol. 2011 Jan; 102(2):1329-37. PMID: 20884206.
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      147. Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams P, Singh AK. A microscale platform for integrated cell-free expression and activity screening of cellulases. J Proteome Res. 2010 Nov 05; 9(11):5677-83. PMID: 20735086.
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      148. Kohn JE, Afonine PV, Ruscio JZ, Adams P, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles. PLoS Comput Biol. 2010 Aug 26; 6(8). PMID: 20865158; PMCID: PMC2928775.
      149. Liu H, Pereira JH, Adams P, Sapra R, Simmons BA, Sale KL. Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. FEBS Lett. 2010 Aug 04; 584(15):3431-5. PMID: 20609364.
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      150. Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams P. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. J Struct Biol. 2010 Dec; 172(3):372-9. PMID: 20599513.
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      151. Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams P. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. J Biol Chem. 2010 Sep 03; 285(36):27958-66. PMID: 20573955; PMCID: PMC2934662.
      152. Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams P. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J Appl Crystallogr. 2010 Aug 01; 43(Pt 4):669-676. PMID: 20648263.
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      153. Schmidt M, Schwartzberg AM, Carroll A, Chaibang A, Adams P, Schuck PJ. Raman imaging of cell wall polymers in Arabidopsis thaliana. Biochem Biophys Res Commun. 2010 May 14; 395(4):521-3. PMID: 20394731.
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      154. Nishi K, Lee HJ, Park SY, Bae SJ, Lee SE, Adams P, Rhee JH, Kim JS. Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. FEBS Lett. 2010 Mar 19; 584(6):1097-102. PMID: 20178784.
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      155. Adams P, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010 Feb; 66(Pt 2):213-21. PMID: 20124702; PMCID: PMC2815670.
      156. Ouellet M, Adams P, Keasling JD, Mukhopadhyay A. A rapid and inexpensive labeling method for microarray gene expression analysis. BMC Biotechnol. 2009 Nov 25; 9:97. PMID: 19939278; PMCID: PMC2790446.
      157. Urzhumtsev A, Afonine PV, Adams P. On the use of logarithmic scales for analysis of diffraction data. Acta Crystallogr D Biol Crystallogr. 2009 Dec; 65(Pt 12):1283-91. PMID: 19966414; PMCID: PMC2789003.
      158. Moriarty NW, Grosse-Kunstleve RW, Adams P. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr. 2009 Oct; 65(Pt 10):1074-80. PMID: 19770504; PMCID: PMC2748967.
      159. Adams P, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Recent developments in phasing and structure refinement for macromolecular crystallography. Curr Opin Struct Biol. 2009 Oct; 19(5):566-72. PMID: 19700309; PMCID: PMC2763973.
      160. Pražnikar J, Afonine PV, Guncar G, Adams P, Turk D. Averaged kick maps: less noise, more signal... and probably less bias. Acta Crystallogr D Biol Crystallogr. 2009 Sep; 65(Pt 9):921-31. PMID: 19690370; PMCID: PMC2733881.
      161. Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams P. Automatic multiple-zone rigid-body refinement with a large convergence radius. J Appl Crystallogr. 2009 Aug 01; 42(Pt 4):607-615. PMID: 19649324.
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      162. Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams P. Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius. Acta Crystallogr D Biol Crystallogr. 2009 Aug; 65(Pt 8):744-50. PMID: 19622857; PMCID: PMC2714717.
      163. Terwilliger TC, Adams P, Read RJ, McCoy AJ, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Zwart PH, Hung LW. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr D Biol Crystallogr. 2009 Jun; 65(Pt 6):582-601. PMID: 19465773; PMCID: PMC2685735.
      164. Adams P, Mustyakimov M, Afonine PV, Langan P. Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. Acta Crystallogr D Biol Crystallogr. 2009 Jun; 65(Pt 6):567-73. PMID: 19465771; PMCID: PMC2685734.
      165. Urzhumtseva L, Afonine PV, Adams P, Urzhumtsev A. Crystallographic model quality at a glance. Acta Crystallogr D Biol Crystallogr. 2009 Mar; 65(Pt 3):297-300. PMID: 19237753; PMCID: PMC2651759.
      166. Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams P, Carter LG, Minor W, Nair R, La Baer J. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. 2009 Jan; 37(Database issue):D365-8. PMID: 19010965; PMCID: PMC2686438.
      167. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams P, Read RJ, Zwart PH, Hung LW. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallogr D Biol Crystallogr. 2008 May; 64(Pt 5):515-24. PMID: 18453687; PMCID: PMC2424225.
      168. Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams P, Afonine PV, Bennett B, Dealwis C, Schoenborn BP. Protein structures by spallation neutron crystallography. J Synchrotron Radiat. 2008 May; 15(Pt 3):215-8. PMID: 18421142; PMCID: PMC2394804.
      169. Blanch HW, Adams P, Andrews-Cramer KM, Frommer WB, Simmons BA, Keasling JD. Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. ACS Chem Biol. 2008 Jan 18; 3(1):17-20. PMID: 18205287.
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      170. Rajalingam D, Kathir KM, Ananthamurthy K, Adams P, Kumar TK. A method for the prevention of thrombin-induced degradation of recombinant proteins. Anal Biochem. 2008 Apr 15; 375(2):361-3. PMID: 18279654; PMCID: PMC2614318.
      171. Kim SH, Shin DH, Kim R, Adams P, Chandonia JM. Structural genomics of minimal organisms: pipeline and results. Methods Mol Biol. 2008; 426:475-96. PMID: 18542885.
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      172. Zwart PH, Afonine PV, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, McKee E, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC, Adams P. Automated structure solution with the PHENIX suite. Methods Mol Biol. 2008; 426:419-35. PMID: 18542881.
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      173. Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams P. Surprises and pitfalls arising from (pseudo)symmetry. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 64(Pt 1):99-107. PMID: 18094473; PMCID: PMC2394827.
      174. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams P. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr. 2008 Jan; 64(Pt 1):61-9. PMID: 18094468; PMCID: PMC2394820.
      175. Afonine PV, Grosse-Kunstleve RW, Adams P, Lunin VY, Urzhumtsev A. On macromolecular refinement at subatomic resolution with interatomic scatterers. Acta Crystallogr D Biol Crystallogr. 2007 Nov; 63(Pt 11):1194-7. PMID: 18007035; PMCID: PMC2808317.
      176. McCoy AJ, Grosse-Kunstleve RW, Adams P, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. 2007 08 01; 40(Pt 4):658-674. PMID: 19461840.
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      177. Oganesyan V, Adams P, Jancarik J, Kim R, Kim SH. Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 May 01; 63(Pt 5):369-74. PMID: 17565173; PMCID: PMC2335016.
      178. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams P, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallogr D Biol Crystallogr. 2007 May; 63(Pt 5):597-610. PMID: 17452785; PMCID: PMC2483474.
      179. Terwilliger TC, Adams P, Moriarty NW, Cohn JD. Ligand identification using electron-density map correlations. Acta Crystallogr D Biol Crystallogr. 2007 Jan; 63(Pt 1):101-7. PMID: 17164532; PMCID: PMC2483487.
      180. Terwilliger TC, Klei H, Adams P, Moriarty NW, Cohn JD. Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr D Biol Crystallogr. 2006 Aug; 62(Pt 8):915-22. PMID: 16855309; PMCID: PMC2745883.
      181. Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams P, Ludtke SJ. SPARX, a new environment for Cryo-EM image processing. J Struct Biol. 2007 Jan; 157(1):47-55. PMID: 16931051.
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      182. Adams P, Oswald RE. Solution structure of an oncogenic mutant of Cdc42Hs. Biochemistry. 2006 Feb 28; 45(8):2577-83. PMID: 16489751; PMCID: PMC2566826.
      183. Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams P, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science. 2006 Jan 13; 311(5758):195-8. PMID: 16410517.
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      184. Xu QS, Jancarik J, Lou Y, Kuznetsova K, Yakunin AF, Yokota H, Adams P, Kim R, Kim SH. Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate. J Struct Funct Genomics. 2005 Dec; 6(4):269-79. PMID: 16283428.
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      185. Liu J, Lou Y, Yokota H, Adams P, Kim R, Kim SH. Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. J Mol Biol. 2005 Nov 25; 354(2):289-303. PMID: 16242716.
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      186. Aishima J, Russel DS, Guibas LJ, Adams P, Brunger AT. Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta Crystallogr D Biol Crystallogr. 2005 Oct; 61(Pt 10):1354-63. PMID: 16204887.
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      187. Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams P, Pace NR. Crystal structure of a bacterial ribonuclease P RNA. Proc Natl Acad Sci U S A. 2005 Sep 20; 102(38):13392-7. PMID: 16157868; PMCID: PMC1224664.
      188. Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams P, Kim R, Kim SH. Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. J Mol Biol. 2005 Jul 29; 350(5):987-96. PMID: 15979091.
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      189. Oganesyan V, Huang C, Adams P, Jancarik J, Yokota HA, Kim R, Kim SH. Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 01; 61(Pt 7):640-6. PMID: 16511117; PMCID: PMC1952466.
      190. Afonine PV, Grosse-Kunstleve RW, Adams P. A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr D Biol Crystallogr. 2005 Jul; 61(Pt 7):850-5. PMID: 15983406; PMCID: PMC2808320.
      191. Oganesyan V, Oganesyan N, Adams P, Jancarik J, Yokota HA, Kim R, Kim SH. Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. J Bacteriol. 2005 Jun; 187(12):4238-44. PMID: 15937186; PMCID: PMC1151740.
      192. Kim JS, DeGiovanni A, Jancarik J, Adams P, Yokota H, Kim R, Kim SH. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc Natl Acad Sci U S A. 2005 Mar 01; 102(9):3248-53. PMID: 15728358; PMCID: PMC549290.
      193. Liu J, Lou Y, Yokota H, Adams P, Kim R, Kim SH. Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. J Biol Chem. 2005 Apr 22; 280(16):15960-6. PMID: 15716271.
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      194. Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams P, Kim R. Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics. 2005; 6(2-3):63-70. PMID: 16211501.
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      195. Chaudhry C, Horwich AL, Brunger AT, Adams P. Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol. 2004 Sep 03; 342(1):229-45. PMID: 15313620.
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      196. Adams P, Loh AP, Oswald RE. Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site. Biochemistry. 2004 Aug 10; 43(31):9968-77. PMID: 15287724.
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      197. Sauter NK, Grosse-Kunstleve RW, Adams P. Robust indexing for automatic data collection. J Appl Crystallogr. 2004 Jun 01; 37(Pt 3):399-409. PMID: 20090869.
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      198. Kochva U, Leonov H, Arkin IT, Adams P. Modeling membrane proteins utilizing information from silent amino acid substitutions. Curr Protoc Bioinformatics. 2004 Feb; Chapter 5:Unit5.3. PMID: 18428728.
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      199. Kwon YD, Nagy I, Adams P, Baumeister W, Jap BK. Crystal structures of the Rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome assembly. J Mol Biol. 2004 Jan 02; 335(1):233-45. PMID: 14659753.
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      200. Grosse-Kunstleve RW, Sauter NK, Adams P. Numerically stable algorithms for the computation of reduced unit cells. Acta Crystallogr A. 2004 Jan; 60(Pt 1):1-6. PMID: 14691322.
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      201. Adams P, Gopal K, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Pai RK, Read RJ, Romo TD, Sacchettini JC, Sauter NK, Storoni LC, Terwilliger TC. Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat. 2004 Jan 01; 11(Pt 1):53-5. PMID: 14646133.
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      202. Grosse-Kunstleve RW, Adams P. Substructure search procedures for macromolecular structures. Acta Crystallogr D Biol Crystallogr. 2003 Nov; 59(Pt 11):1966-73. PMID: 14573951.
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      203. Grosse-Kunstleve RW, Adams P. On symmetries of substructures. Acta Crystallogr D Biol Crystallogr. 2003 Nov; 59(Pt 11):1974-7. PMID: 14573952.
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      204. Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams P, Horwich AL, Sigler PB. Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO J. 2003 Oct 01; 22(19):4877-87. PMID: 14517228; PMCID: PMC204461.
      205. Pauly TA, Ekstrom JL, Beebe DA, Chrunyk B, Cunningham D, Griffor M, Kamath A, Lee SE, Madura R, Mcguire D, Subashi T, Wasilko D, Watts P, Mylari BL, Oates PJ, Adams P, Rath VL. X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure. 2003 Sep; 11(9):1071-85. PMID: 12962626.
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      206. Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams P, Pace NR. High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A. 2003 Jun 24; 100(13):7497-502. PMID: 12799461; PMCID: PMC164615.
      207. Weeks CM, Adams P, Berendzen J, Brunger AT, Dodson EJ, Grosse-Kunstleve RW, Schneider TR, Sheldrick GM, Terwilliger TC, Turkenburg MG, Usón I. Automatic solution of heavy-atom substructures. Methods Enzymol. 2003; 374:37-83. PMID: 14696368.
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      208. Adams P, Grosse-Kunstleve RW, Brunger AT. Computational aspects of high-throughput crystallographic macromolecular structure determination. Methods Biochem Anal. 2003; 44:75-87. PMID: 12647382.
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      209. Adams P, Grosse-Kunstleve RW, Hung LW, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr. 2002 Nov; 58(Pt 11):1948-54. PMID: 12393927.
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      210. Adams P, Chen Y, Ma K, Zagorski MG, Sönnichsen FD, McLaughlin ML, Barkley MD. Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. J Am Chem Soc. 2002 Aug 07; 124(31):9278-86. PMID: 12149035.
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      211. Gottschalk KE, Adams P, Brunger AT, Kessler H. Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci. 2002 Jul; 11(7):1800-12. PMID: 12070332; PMCID: PMC2373644.
      212. Brunger AT, Adams P. Molecular dynamics applied to X-ray structure refinement. Acc Chem Res. 2002 Jun; 35(6):404-12. PMID: 12069625.
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      213. Grosse-Kunstleve RW, Adams P. Algorithms for deriving crystallographic space-group information. II. Treatment of special positions. Acta Crystallogr A. 2002 Jan; 58(Pt 1):60-5. PMID: 11752765.
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      214. Grosse-Kunstleve RW, Adams P. Patterson correlation methods: a review of molecular replacement with CNS. Acta Crystallogr D Biol Crystallogr. 2001 Oct; 57(Pt 10):1390-6. PMID: 11567150.
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      215. Adams P, Grosse-Kunstleve RW. Recent developments in software for the automation of crystallographic macromolecular structure determination. Curr Opin Struct Biol. 2000 Oct; 10(5):564-8. PMID: 11042455.
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