Paul David Adams - Publications

Affiliations: 
1999- Molecular Biophysics & Integrated Bioimaging Lawrence Berkeley National Laboratory, Berkeley, CA, USA 
 2007- Bioengineering University of California, Berkeley, Berkeley, CA 
Area:
crystallography, cryo-EM, computational methods, structural biology
Website:
http://cci.lbl.gov/~paul/

130 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 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. Nature Methods. PMID 36266465 DOI: 10.1038/s41592-022-01645-6  0.759
2021 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, ... ... Adams PD, et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science (New York, N.Y.). PMID 34282049 DOI: 10.1126/science.abj8754  0.526
2021 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. Scientific Reports. 11: 11803. PMID 34083602 DOI: 10.1038/s41598-021-91181-8  0.516
2021 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. Biotechnology For Biofuels. 14: 108. PMID 33926536 DOI: 10.1186/s13068-021-01953-7  0.482
2021 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. Frontiers in Microbiology. 12: 642422. PMID 33841364 DOI: 10.3389/fmicb.2021.642422  0.435
2021 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, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. PMID 33542514 DOI: 10.1038/s41592-020-01051-w  0.545
2021 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 Crystallographica. Section D, Structural Biology. 77: 48-61. PMID 33404525 DOI: 10.1107/S2059798320015879  0.752
2020 Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Gushgari-Doyle S, Lui LM, Nielsen T, Chakraborty R, Adams PD, Arkin AP, Hazen TC, Adams MWW. Characterization of a Metal-Resistant Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation. Frontiers in Microbiology. 11: 587127. PMID 33193240 DOI: 10.3389/fmicb.2020.587127  0.394
2020 Ge X, Thorgersen MP, Poole FL, Deutschbauer AM, Chandonia JM, Novichkov PS, Adams PD, Arkin AP, Hazen TC, Adams MWW. Draft Genome Sequence of sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment. Microbiology Resource Announcements. 9. PMID 33122416 DOI: 10.1128/MRA.01149-20  0.375
2020 Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Read RJ. Density modification of cryo-EM maps. Acta Crystallographica. Section D, Structural Biology. 76: 912-925. PMID 33021493 DOI: 10.1107/S205979832001061X  0.491
2020 Terwilliger TC, Ludtke SJ, Read RJ, Adams PD, Afonine PV. Improvement of cryo-EM maps by density modification. Nature Methods. 17: 923-927. PMID 32807957 DOI: 10.1038/S41592-020-0914-9  0.5
2020 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, ... ... Adams PD, et al. An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism. Nature Communications. 11: 2931. PMID 32523014 DOI: 10.1038/S41467-020-16815-3  0.437
2020 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, ... ... Adams PD, et al. Untangling the sequence of events during the S → S transition in photosystem II and implications for the water oxidation mechanism. Proceedings of the National Academy of Sciences of the United States of America. PMID 32434915 DOI: 10.1073/Pnas.2000529117  0.494
2020 Park MR, Chen Y, Thompson M, Benites V, Fong B, Petzold C, Baidoo E, Gladden J, Adams P, Keasling J, Simmons BA, Singer SW. The response of Pseudomonas putida to complex aromatic-rich fractions from biomass. Chemsuschem. PMID 32160408 DOI: 10.1002/Cssc.202000268  0.382
2020 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 Crystallographica. Section D, Structural Biology. 76: 51-62. PMID 31909743 DOI: 10.1107/S2059798319015134  0.541
2019 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, et al. Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase. Journal of the American Chemical Society. PMID 31793780 DOI: 10.1021/Jacs.9B09187  0.422
2019 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, ... ... Adams PD, et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallographica. Section D, Structural Biology. 75: 861-877. PMID 31588918 DOI: 10.1107/S2059798319011471  0.812
2019 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. Metabolic Engineering. PMID 31499175 DOI: 10.1016/J.Ymben.2019.09.003  0.36
2019 Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, Garcia Martin H, Hillson NJ, Petzold CJ. An automated 'cells-to-peptides' sample preparation workflow for high-throughput, quantitative proteomic assays of microbes. Journal of Proteome Research. PMID 31436101 DOI: 10.1021/Acs.Jproteome.9B00455  0.385
2019 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. Journal of Structural Biology. PMID 31279069 DOI: 10.1016/J.Jsb.2019.05.012  0.722
2019 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. Journal of Industrial Microbiology & Biotechnology. PMID 31115703 DOI: 10.1007/S10295-019-02189-Z  0.416
2019 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, Henrique Pereira J, Baidoo EEK, ... ... Adams PD, et al. Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Lysine Metabolism. Mbio. 10. PMID 31064836 DOI: 10.1128/Mbio.02577-18  0.555
2019 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, et al. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallographica. Section D, Structural Biology. 75: 451-454. PMID 30988261 DOI: 10.1107/S2059798319004522  0.683
2019 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. 14: e0211582. PMID 30763335 DOI: 10.1371/Journal.Pone.0211582  0.428
2018 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 . Biotechnology For Biofuels. 11: 285. PMID 30377444 DOI: 10.1186/S13068-018-1272-Z  0.35
2018 Ge X, Vaccaro BJ, Thorgersen MP, Poole FL, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, et al. Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle. Environmental Microbiology. PMID 30289197 DOI: 10.1111/1462-2920.14435  0.377
2018 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). Biotechnology For Biofuels. 11: 266. PMID 30275906 DOI: 10.1186/S13068-018-1261-2  0.521
2018 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 Crystallographica. Section D, Structural Biology. 74: 814-840. PMID 30198894 DOI: 10.1107/S2059798318009324  0.725
2018 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 Crystallographica. Section D, Structural Biology. 74: 531-544. PMID 29872004 DOI: 10.1107/S2059798318006551  0.776
2018 Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD. Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nature Chemical Biology. PMID 29556105 DOI: 10.1038/S41589-018-0017-4  0.373
2018 George KW, Thompson M, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS. Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. Metabolic Engineering. PMID 29530749 DOI: 10.1016/J.Ymben.2018.03.004  0.397
2018 Chodkiewicz ML, Migacz S, Rudnicki W, Makal A, Kalinowski JA, Moriarty NW, Grosse-Kunstleve RW, Afonine PV, Adams PD, Dominiak PM. : a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. Journal of Applied Crystallography. 51: 193-199. PMID 29507550 DOI: 10.1107/S1600576717015825  0.304
2018 He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, ... ... Adams PD, et al. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. Mbio. 9. PMID 29463661 DOI: 10.1128/Mbio.02435-17  0.398
2017 Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, 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. Biotechnology and Bioengineering. PMID 29278415 DOI: 10.1002/Bit.26530  0.375
2017 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 PD, et al. MolProbity: More and better reference data for improved all-atom structure validation. Protein Science : a Publication of the Protein Society. PMID 29067766 DOI: 10.1002/Pro.3330  0.789
2017 Moriarty NW, Liebschner D, Klei HE, Echols N, Afonine PV, Headd J, Poon BK, Adams PD. Interactive Comparison and Remediation of Collections of Macromolecular Structures. Protein Science : a Publication of the Protein Society. PMID 28901593 DOI: 10.1002/Pro.3296  0.794
2017 Morrell W, Birkel G, Forrer M, Lopez T, Backman T, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso Gutierrez J, George K, Mukhopadhyay A, Vaino I, Keasling JD, ... Adams PD, et al. The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization. Acs Synthetic Biology. PMID 28826210 DOI: 10.1021/Acssynbio.7B00204  0.44
2017 Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EE, Wang G, Chan LJ, Adams PD, Petzold CJ, Keasling JD, Lee TS. Production of jet fuel precursor monoterpenoids from engineered Escherichia coli. Biotechnology and Bioengineering. PMID 28369701 DOI: 10.1002/Bit.26296  0.374
2017 Liebschner D, Afonine PV, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD. Polder maps: improving OMIT maps by excluding bulk solvent. Acta Crystallographica. Section D, Structural Biology. 73: 148-157. PMID 28177311 DOI: 10.1107/S2059798316018210  0.727
2016 Heinemann J, Deng K, Shih SC, Gao J, Adams PD, Singh AK, Northen TR. On-chip integration of droplet microfluidics and nanostructure-initiator mass spectrometry for enzyme screening. Lab On a Chip. PMID 27957569 DOI: 10.1039/C6Lc01182A  0.513
2016 Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller FD, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, ... ... Adams PD, et al. Structure of photosystem II and substrate binding at room temperature. Nature. PMID 27871088 DOI: 10.1038/Nature20161  0.62
2016 Hiras J, Wu YW, Deng K, Nicora CD, Aldrich JT, Frey D, Kolinko S, Robinson EW, Jacobs JM, Adams PD, 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. 7. PMID 27555310 DOI: 10.1128/Mbio.01106-16  0.513
2016 Yuzawa S, Deng K, Wang G, Baidoo EE, Northen TR, Adams PD, 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 Synthetic Biology. PMID 27548700 DOI: 10.1021/Acssynbio.6B00176  0.603
2016 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 PD, et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. PMID 27211860 DOI: 10.1016/J.Cels.2016.04.004  0.399
2016 Sauter NK, Echols N, Adams PD, 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. 533: E1-2. PMID 27193689 DOI: 10.1038/Nature17983  0.568
2016 Adams PD, 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, et al. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure (London, England : 1993). 24: 502-8. PMID 27050687 DOI: 10.1016/J.Str.2016.02.017  0.513
2016 Eudes A, Pereira JH, Yogiswara S, Wang G, Teixeira Benites V, Baidoo EE, Lee TS, Adams PD, Keasling JD, Loqué D. Exploiting The Substrate Promiscuity of Hydroxycinnamoyl-CoA:shikimate Hydroxycinnamoyl Transferase to Reduce Lignin. Plant & Cell Physiology. PMID 26858288 DOI: 10.1093/Pcp/Pcw016  0.415
2016 Gach PC, Shih SC, Sustarich J, Keasling JD, Hillson NJ, Adams PD, Singh AK. A Droplet Microfluidic Platform for Automating Genetic Engineering. Acs Synthetic Biology. PMID 26830031 DOI: 10.1021/Acssynbio.6B00011  0.386
2015 Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. Biotechnology For Biofuels. 8: 220. PMID 26697109 DOI: 10.1186/S13068-015-0402-0  0.515
2015 Deng K, Takasuka TE, Bianchetti CM, Bergeman LF, Adams PD, Northen TR, Fox BG. Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases. Frontiers in Bioengineering and Biotechnology. 3: 165. PMID 26579511 DOI: 10.3389/Fbioe.2015.00165  0.524
2015 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, ... ... Adams PD, et al. Development of a High Throughput Platform for Screening Glycoside Hydrolases Based on Oxime-NIMS. Frontiers in Bioengineering and Biotechnology. 3: 153. PMID 26528471 DOI: 10.3389/Fbioe.2015.00153  0.535
2015 Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature Methods. 12: 943-6. PMID 26280328 DOI: 10.1038/Nmeth.3541  0.654
2015 Shih SC, Goyal G, Kim PW, Koutsoubelis N, Keasling JD, Adams PD, Hillson NJ, Singh AK. A Versatile Microfluidic Device for Automating Synthetic Biology. Acs Synthetic Biology. PMID 26075958 DOI: 10.1021/Acssynbio.5B00062  0.396
2015 George KW, Thompson MG, Kang A, Baidoo E, Wang G, Chan LJ, Adams PD, Petzold CJ, Keasling JD, Lee TS. Metabolic engineering for the high-yield production of isoprenoid-based C₅ alcohols in E. coli. Scientific Reports. 5: 11128. PMID 26052683 DOI: 10.1038/Srep11128  0.359
2015 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, ... ... Adams PD, et al. Natural bacterial communities serve as quantitative geochemical biosensors. Mbio. 6: e00326-15. PMID 25968645 DOI: 10.1128/Mbio.00326-15  0.409
2015 Morshed N, Echols N, Adams PD. Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 71: 1147-58. PMID 25945580 DOI: 10.1107/S1399004715004241  0.657
2015 Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. Acta Crystallographica. Section D, Biological Crystallography. 71: 357-66. PMID 25664747 DOI: 10.1107/S1399004714026145  0.64
2015 Alonso-Gutierrez J, Kim EM, Batth TS, Cho N, Hu Q, Chan LJ, Petzold CJ, Hillson NJ, Adams PD, Keasling JD, Garcia Martin H, Lee TS. Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering. Metabolic Engineering. 28: 123-33. PMID 25554074 DOI: 10.1016/J.Ymben.2014.11.011  0.42
2015 Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nature Methods. 12: 127-30. PMID 25532136 DOI: 10.1038/Nmeth.3212  0.745
2014 Sauter NK, Hattne J, Brewster AS, Echols N, Zwart PH, Adams PD. Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallographica. Section D, Biological Crystallography. 70: 3299-309. PMID 25478847 DOI: 10.1107/S1399004714024134  0.647
2014 Poust S, Yoon I, Adams PD, 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. 9: e109421. PMID 25286165 DOI: 10.1371/Journal.Pone.0109421  0.402
2014 Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams PD, Petzold CJ, Katz L, Keasling JD. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metabolic Engineering. 26: 111-118. PMID 25250846 DOI: 10.1016/J.Ymben.2014.09.002  0.377
2014 Batth TS, Singh P, Ramakrishnan VR, Sousa MM, Chan LJ, Tran HM, Luning EG, Pan EH, Vuu KM, Keasling JD, Adams PD, Petzold CJ. A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins. Metabolic Engineering. 26: 48-56. PMID 25205128 DOI: 10.1016/J.Ymben.2014.08.004  0.406
2014 Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams PD, Petzold CJ, Keasling JD. In vitro analysis of carboxyacyl substrate tolerance in the loading and first extension modules of borrelidin polyketide synthase. Biochemistry. 53: 5975-7. PMID 25188840 DOI: 10.1021/Bi500951C  0.364
2014 Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. Plos Computational Biology. 10: e1003827. PMID 25188426 DOI: 10.1371/Journal.Pcbi.1003827  0.365
2014 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, ... ... Adams PD, et al. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nature Communications. 5: 4371. PMID 25006873 DOI: 10.1038/Ncomms5371  0.625
2014 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, ... ... Adams PD, et al. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. Acs Chemical Biology. 9: 2082-91. PMID 24984213 DOI: 10.1021/Cb500244V  0.527
2014 Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. Plos One. 9: e101115. PMID 24983352 DOI: 10.1371/Journal.Pone.0101115  0.357
2014 Kung Y, McAndrew RP, Xie X, Liu CC, Pereira JH, Adams PD, Keasling JD. Constructing tailored isoprenoid products by structure-guided modification of geranylgeranyl reductase. Structure (London, England : 1993). 22: 1028-36. PMID 24954619 DOI: 10.1016/J.Str.2014.05.007  0.459
2014 Deng K, Takasuka TE, Heins R, Cheng X, Bergeman LF, Shi J, Aschenbrener R, Deutsch S, Singh S, Sale KL, Simmons BA, Adams PD, Singh AK, Fox BG, Northen TR. Rapid kinetic characterization of glycosyl hydrolases based on oxime derivatization and nanostructure-initiator mass spectrometry (NIMS). Acs Chemical Biology. 9: 1470-9. PMID 24819174 DOI: 10.1021/Cb5000289  0.536
2014 Headd JJ, Echols N, Afonine PV, Moriarty NW, Gildea RJ, Adams PD. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallographica. Section D, Biological Crystallography. 70: 1346-56. PMID 24816103 DOI: 10.1107/S1399004714003277  0.8
2014 Echols N, Morshed N, Afonine PV, McCoy AJ, Miller MD, Read RJ, Richardson JS, Terwilliger TC, Adams PD. Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 70: 1104-14. PMID 24699654 DOI: 10.1107/S1399004714001308  0.76
2014 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, ... ... Adams PD, et al. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods. 11: 545-8. PMID 24633409 DOI: 10.1038/Nmeth.2887  0.645
2014 George KW, Chen A, Jain A, Batth TS, Baidoo EE, Wang G, Adams PD, Petzold CJ, Keasling JD, Lee TS. Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production. Biotechnology and Bioengineering. 111: 1648-58. PMID 24615242 DOI: 10.1002/Bit.25226  0.416
2014 Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography. 70: 144-54. PMID 24419387 DOI: 10.1107/S139900471302748X  0.795
2014 Klei HE, Moriarty NW, Echols N, Terwilliger TC, Baldwin ET, Pokross M, Posy S, Adams PD. Ligand placement based on prior structures: the guided ligand-replacement method Acta Crystallographica Section D: Biological Crystallography. 70: 134-143. PMID 24419386 DOI: 10.1107/S1399004713030071  0.66
2014 Ito J, Herter T, Baidoo EE, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams PD, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Analytical Biochemistry. 448: 14-22. PMID 24299991 DOI: 10.1016/J.Ab.2013.11.026  0.381
2014 Javidpour P, Pereira JH, Goh EB, McAndrew RP, Ma SM, Friedland GD, Keasling JD, Chhabra SR, Adams PD, Beller HR. Biochemical and structural studies of NADH-dependent FabG used to increase the bacterial production of fatty acids under anaerobic conditions. Applied and Environmental Microbiology. 80: 497-505. PMID 24212572 DOI: 10.1128/Aem.03194-13  0.385
2013 Cheng X, Hiras J, Deng K, Bowen B, Simmons BA, Adams PD, Singer SW, Northen TR. High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production. Frontiers in Microbiology. 4: 365. PMID 24367356 DOI: 10.3389/Fmicb.2013.00365  0.517
2013 Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ. Phaser.MRage: automated molecular replacement. Acta Crystallographica. Section D, Biological Crystallography. 69: 2276-86. PMID 24189240 DOI: 10.1107/S0907444913022750  0.721
2013 Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Hung LW. Model morphing and sequence assignment after molecular replacement. Acta Crystallographica. Section D, Biological Crystallography. 69: 2244-50. PMID 24189236 DOI: 10.1107/S0907444913017770  0.667
2013 Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nature Biotechnology. 31: 1039-46. PMID 24142050 DOI: 10.1038/Nbt.2689  0.378
2013 DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D. Improved low-resolution crystallographic refinement with Phenix and Rosetta. Nature Methods. 10: 1102-4. PMID 24076763 DOI: 10.1107/S2053273314092171  0.798
2013 Alonso-Gutierrez J, Chan R, Batth TS, Adams PD, Keasling JD, Petzold CJ, Lee TS. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Metabolic Engineering. 19: 33-41. PMID 23727191 DOI: 10.1016/J.Ymben.2013.05.004  0.359
2013 McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. The Journal of Biological Chemistry. 288: 14985-92. PMID 23580647 DOI: 10.1074/Jbc.M113.458356  0.539
2013 Adams PD, 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. Annual Review of Biophysics. 42: 265-87. PMID 23451892 DOI: 10.1146/Annurev-Biophys-083012-130253  0.739
2013 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, ... ... Adams PD, et al. Simultaneous femtosecond X-ray spectroscopy and diffraction of photosystem II at room temperature. Science (New York, N.Y.). 340: 491-5. PMID 23413188 DOI: 10.1126/Science.1234273  0.632
2013 Read RJ, Adams PD, McCoy AJ. Intensity statistics in the presence of translational noncrystallographic symmetry. Acta Crystallographica. Section D, Biological Crystallography. 69: 176-83. PMID 23385454 DOI: 10.1107/S0907444912045374  0.494
2012 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, ... ... Adams PD, et al. Energy-dispersive X-ray emission spectroscopy using an X-ray free-electron laser in a shot-by-shot mode. Proceedings of the National Academy of Sciences of the United States of America. 109: 19103-7. PMID 23129631 DOI: 10.1073/Pnas.1211384109  0.641
2012 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, ... ... Adams PD, et al. Nanoflow electrospinning serial femtosecond crystallography. Acta Crystallographica. Section D, Biological Crystallography. 68: 1584-7. PMID 23090408 DOI: 10.1107/S0907444912038152  0.615
2012 Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling JD. Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metabolic Engineering. 14: 653-60. PMID 23026122 DOI: 10.1016/J.Ymben.2012.08.009  0.345
2012 Pereira JH, Goh EB, Keasling JD, Beller HR, Adams PD. Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus. Acta Crystallographica. Section D, Biological Crystallography. 68: 1320-8. PMID 22993086 DOI: 10.1107/S0907444912028351  0.426
2012 Terwilliger TC, Read RJ, Adams PD, Brunger AT, Afonine PV, Grosse-Kunstleve RW, Hung LW. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. Acta Crystallographica. Section D, Biological Crystallography. 68: 861-70. PMID 22751672 DOI: 10.1107/S0907444912015636  0.688
2012 McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microbial Cell Factories. 11: 79. PMID 22694848 DOI: 10.1186/1475-2859-11-79  0.543
2012 Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schröder GF. Improving the accuracy of macromolecular structure refinement at 7 Ã… resolution. Structure (London, England : 1993). 20: 957-66. PMID 22681901 DOI: 10.1016/J.Str.2012.04.020  0.568
2012 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 PD. Graphical tools for macromolecular crystallography in PHENIX. Journal of Applied Crystallography. 45: 581-586. PMID 22675231 DOI: 10.1107/S0021889812017293  0.76
2012 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, ... ... Adams PD, et al. Room temperature femtosecond X-ray diffraction of photosystem II microcrystals. Proceedings of the National Academy of Sciences of the United States of America. 109: 9721-6. PMID 22665786 DOI: 10.1073/Pnas.1204598109  0.623
2012 Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, 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. The Journal of Biological Chemistry. 287: 25335-43. PMID 22645145 DOI: 10.1074/Jbc.M112.362640  0.554
2012 Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics. 12: 1289-99. PMID 22577029 DOI: 10.1002/Pmic.201100482  0.398
2012 Brunger AT, Das D, Deacon AM, Grant J, Terwilliger TC, Read RJ, Adams PD, 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 Crystallographica. Section D, Biological Crystallography. 68: 391-403. PMID 22505259 DOI: 10.1107/S090744491104978X  0.671
2012 Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica. Section D, Biological Crystallography. 68: 381-90. PMID 22505258 DOI: 10.1107/S0907444911047834  0.798
2012 Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallographica. Section D, Biological Crystallography. 68: 352-67. PMID 22505256 DOI: 10.1107/S0907444912001308  0.808
2012 Terwilliger TC, Dimaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. Journal of Structural and Functional Genomics. 13: 81-90. PMID 22418934 DOI: 10.1007/S10969-012-9129-3  0.735
2012 Greving M, Cheng X, Reindl W, Bowen B, Deng K, Louie K, Nyman M, Cohen J, Singh A, Simmons B, Adams P, Siuzdak G, Northen T. Acoustic deposition with NIMS as a high-throughput enzyme activity assay. Analytical and Bioanalytical Chemistry. 403: 707-11. PMID 22407334 DOI: 10.1007/S00216-012-5908-8  0.519
2012 Deng K, George KW, Reindl W, Keasling JD, Adams PD, Lee TS, Singh AK, Northen TR. Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme. Rapid Communications in Mass Spectrometry : Rcm. 26: 611-5. PMID 22328213 DOI: 10.1002/Rcm.6134  0.594
2012 Groff D, Benke PI, Batth TS, Bokinsky G, Petzold CJ, Adams PD, Keasling JD. Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars. Applied and Environmental Microbiology. 78: 2221-9. PMID 22286982 DOI: 10.1128/Aem.06761-11  0.358
2011 McAndrew RP, Peralta-Yahya PP, DeGiovanni A, Pereira JH, Hadi MZ, Keasling JD, Adams PD. Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production. Structure (London, England : 1993). 19: 1876-84. PMID 22153510 DOI: 10.1016/J.Str.2011.09.013  0.465
2011 Read RJ, Adams PD, 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, et al. A new generation of crystallographic validation tools for the protein data bank. Structure (London, England : 1993). 19: 1395-412. PMID 22000512 DOI: 10.1016/J.Str.2011.08.006  0.735
2011 Adams PD, Afonine PV, Bunkóczi G, Chen VB, Echols N, Headd JJ, Hung LW, Jain S, Kapral GJ, Grosse Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner RD, Read RJ, Richardson DC, et al. The Phenix software for automated determination of macromolecular structures. Methods (San Diego, Calif.). 55: 94-106. PMID 21821126 DOI: 10.1016/J.Ymeth.2011.07.005  0.804
2011 Redding-Johanson AM, Batth TS, Chan R, Krupa R, Szmidt HL, Adams PD, Keasling JD, Lee TS, Mukhopadhyay A, Petzold CJ. Targeted proteomics for metabolic pathway optimization: application to terpene production. Metabolic Engineering. 13: 194-203. PMID 21215324 DOI: 10.1016/J.Ymben.2010.12.005  0.399
2010 Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. Journal of Applied Crystallography. 43: 669-676. PMID 20648263 DOI: 10.1107/S0021889810015608  0.766
2010 Adams PD, 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, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica. Section D, Biological Crystallography. 66: 213-21. PMID 20124702 DOI: 10.1107/S0907444909052925  0.79
2009 Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. A rapid and inexpensive labeling method for microarray gene expression analysis. Bmc Biotechnology. 9: 97. PMID 19939278 DOI: 10.1186/1472-6750-9-97  0.38
2009 Adams PD, Afonine PV, Grosse-Kunstleve RW, Read RJ, Richardson JS, Richardson DC, Terwilliger TC. Recent developments in phasing and structure refinement for macromolecular crystallography. Current Opinion in Structural Biology. 19: 566-72. PMID 19700309 DOI: 10.1016/J.Sbi.2009.07.014  0.662
2009 Terwilliger TC, Adams PD, 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 Crystallographica. Section D, Biological Crystallography. 65: 582-601. PMID 19465773 DOI: 10.1107/S0907444909012098  0.484
2008 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 PD. Automated structure solution with the PHENIX suite. Methods in Molecular Biology (Clifton, N.J.). 426: 419-35. PMID 18542881 DOI: 10.1007/978-1-60327-058-8_28  0.589
2008 Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Adams PD, Read RJ, Zwart PH, Hung LW. Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. Acta Crystallographica. Section D, Biological Crystallography. 64: 515-24. PMID 18453687 DOI: 10.1107/S0907444908004319  0.553
2008 Blanch HW, Adams PD, Andrews-Cramer KM, Frommer WB, Simmons BA, Keasling JD. Addressing the need for alternative transportation fuels: the Joint BioEnergy Institute. Acs Chemical Biology. 3: 17-20. PMID 18205287 DOI: 10.1021/Cb700267S  0.332
2008 Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung LW, Read RJ, Adams PD. Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallographica. Section D, Biological Crystallography. 64: 61-9. PMID 18094468 DOI: 10.1107/S090744490705024X  0.557
2007 McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. Journal of Applied Crystallography. 40: 658-674. PMID 19461840 DOI: 10.1107/S0021889807021206  0.484
2007 Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallographica. Section D, Biological Crystallography. 63: 597-610. PMID 17452785 DOI: 10.1107/S0907444907009791  0.575
2005 Aishima J, Russel DS, Guibas LJ, Adams PD, Brunger AT. Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface. Acta Crystallographica. Section D, Biological Crystallography. 61: 1354-63. PMID 16204887 DOI: 10.1107/S0907444905023152  0.511
2004 Chaudhry C, Horwich AL, Brunger AT, Adams PD. Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. Journal of Molecular Biology. 342: 229-45. PMID 15313620 DOI: 10.1016/J.Jmb.2004.07.015  0.723
2004 Adams PD, 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. Journal of Synchrotron Radiation. 11: 53-5. PMID 14646133 DOI: 10.1107/S0909049503024130  0.551
2003 Weeks CM, Adams PD, 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 in Enzymology. 374: 37-83. PMID 14696368 DOI: 10.1016/S0076-6879(03)74003-8  0.514
2003 Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams PD, Horwich AL, Sigler PB. Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. The Embo Journal. 22: 4877-87. PMID 14517228 DOI: 10.1093/Emboj/Cdg477  0.774
2003 Adams PD, Grosse-Kunstleve RW, Brunger AT. Computational aspects of high-throughput crystallographic macromolecular structure determination. Methods of Biochemical Analysis. 44: 75-87. PMID 12647382  0.509
2002 Adams PD, 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 Crystallographica. Section D, Biological Crystallography. 58: 1948-54. PMID 12393927 DOI: 10.1107/S0907444902016657  0.561
2002 Gottschalk KE, Adams PD, Brunger AT, Kessler H. Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Science : a Publication of the Protein Society. 11: 1800-12. PMID 12070332 DOI: 10.1110/Ps.4120102  0.454
2002 Brunger AT, Adams PD. Molecular dynamics applied to X-ray structure refinement. Accounts of Chemical Research. 35: 404-12. PMID 12069625 DOI: 10.1021/ar010034r  0.503
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