| Year |
Citation |
Score |
| 2024 |
Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, et al. Community recommendations on cryoEM data archiving and validation. Iucrj. PMID 38358351 DOI: 10.1107/S2052252524001246 |
0.512 |
|
| 2024 |
Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, ... ... Adams PD, et al. Environmental stress mediates groundwater microbial community assembly. Nature Microbiology. PMID 38212658 DOI: 10.1038/s41564-023-01573-x |
0.39 |
|
| 2023 |
Kleywegt GJ, Adams PD, Butcher SJ, Lawson C, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, et al. Community recommendations on cryoEM data archiving and validation. Arxiv. PMID 38076521 |
0.512 |
|
| 2023 |
Terwilliger TC, Liebschner D, Croll TI, Williams CJ, McCoy AJ, Poon BK, Afonine PV, Oeffner RD, Richardson JS, Read RJ, Adams PD. AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination. Nature Methods. PMID 38036854 DOI: 10.1038/s41592-023-02087-4 |
0.779 |
|
| 2023 |
Liebschner D, Afonine PV, Poon BK, Moriarty NW, Adams PD. Improved joint X-ray and neutron refinement procedure in Phenix. Acta Crystallographica. Section D, Structural Biology. PMID 37942718 DOI: 10.1107/S2059798323008914 |
0.707 |
|
| 2023 |
Chen Y, Gin JW, Wang Y, de Raad M, Tan S, Hillson NJ, Northen TR, Adams PD, Petzold CJ. Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. Plos One. 18: e0288102. PMID 37418444 DOI: 10.1371/journal.pone.0288102 |
0.508 |
|
| 2023 |
Takasuka T, Kim H, Deng K, Bianchetti CM, Yamashita K, Beebe ET, Bergeman LF, Vander Meulen KA, Deutsch S, Ralph J, Adams PD, Northen TR, Fox BG. Quantitative analysis of The High Yield Hydrolysis of Kelp by Laminarinase and Alginate Lyase. Chembiochem : a European Journal of Chemical Biology. e202300357. PMID 37402642 DOI: 10.1002/cbic.202300357 |
0.51 |
|
| 2023 |
Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR. A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. Lab On a Chip. PMID 37401915 DOI: 10.1039/d2lc00980c |
0.487 |
|
| 2023 |
Huang J, Quest A, Cruz-Morales P, Deng K, Pereira JH, Van Cura D, Kakumanu R, Baidoo EEK, Dan Q, Chen Y, Petzold CJ, Northen TR, Adams PD, Clark DS, Balskus EP, et al. Complete integration of carbene-transfer chemistry into biosynthesis. Nature. PMID 37138074 DOI: 10.1038/s41586-023-06027-2 |
0.577 |
|
| 2023 |
Englund E, Schmidt M, Nava AA, Lechner A, Deng K, Jocic R, Lin Y, Roberts J, Benites VT, Kakumanu R, Gin JW, Chen Y, Liu Y, Petzold CJ, Baidoo EEK, ... ... Adams PD, et al. Expanding Extender Substrate Selection for Unnatural Polyketide Biosynthesis by Acyltransferase Domain Exchange within a Modular Polyketide Synthase. Journal of the American Chemical Society. PMID 37057992 DOI: 10.1021/jacs.2c11027 |
0.625 |
|
| 2023 |
Terwilliger TC, Afonine PV, Liebschner D, Croll TI, McCoy AJ, Oeffner RD, Williams CJ, Poon BK, Richardson JS, Read RJ, Adams PD. Accelerating crystal structure determination with iterative AlphaFold prediction. Acta Crystallographica. Section D, Structural Biology. 79: 234-244. PMID 36876433 DOI: 10.1107/S205979832300102X |
0.796 |
|
| 2023 |
Liebschner D, Moriarty NW, Poon BK, Adams PD. In situ ligand restraints from quantum-mechanical methods. Acta Crystallographica. Section D, Structural Biology. 79: 100-110. PMID 36762856 DOI: 10.1107/S2059798323000025 |
0.672 |
|
| 2022 |
Deng K, Wang X, Ing N, Opgenorth P, de Raad M, Kim J, Simmons BA, Adams PD, Singh AK, Lee TS, Northen TR. Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS). Analytical Biochemistry. 114997. PMID 36435200 DOI: 10.1016/j.ab.2022.114997 |
0.47 |
|
| 2022 |
Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, et al. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. Microbiome. 10: 183. PMID 36280858 DOI: 10.1186/s40168-022-01377-x |
0.477 |
|
| 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 |
0.779 |
|
| 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 |
0.498 |
|
| 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 |
0.466 |
|
| 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 |
0.538 |
|
| 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 |
0.733 |
|
| 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 |
0.388 |
|
| 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 |
0.369 |
|
| 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 |
0.484 |
|
| 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 |
0.493 |
|
| 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 |
0.432 |
|
| 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 |
0.475 |
|
| 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 |
0.376 |
|
| 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 |
0.536 |
|
| 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 |
0.419 |
|
| 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 |
0.805 |
|
| 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 |
0.354 |
|
| 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 |
0.38 |
|
| 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 |
0.7 |
|
| 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 |
0.412 |
|
| 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 |
0.549 |
|
| 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 |
0.661 |
|
| 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 |
0.423 |
|
| 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 |
0.345 |
|
| 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 |
0.372 |
|
| 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 |
0.504 |
|
| 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 |
0.703 |
|
| 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 |
0.763 |
|
| 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 |
0.369 |
|
| 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 |
0.391 |
|
| 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 |
0.368 |
|
| 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 |
0.797 |
|
| 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 |
0.368 |
|
| 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 |
0.707 |
|
| 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 |
0.495 |
|
| 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 |
0.619 |
|
| 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 |
0.498 |
|
| 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 |
0.591 |
|
| 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 |
0.392 |
|
| 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 |
0.51 |
|
| 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 |
0.409 |
|
| 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 |
0.38 |
|
| 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 |
0.498 |
|
| 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 |
0.508 |
|
| 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 |
0.52 |
|
| 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 |
0.652 |
|
| 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 |
0.388 |
|
| 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 |
0.354 |
|
| 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 |
0.408 |
|
| 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 |
0.656 |
|
| 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 |
0.639 |
|
| 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 |
0.413 |
|
| 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 |
0.744 |
|
| 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 |
0.395 |
|
| 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 |
0.371 |
|
| 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 |
0.399 |
|
| 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 |
0.358 |
|
| 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 |
0.361 |
|
| 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 |
0.51 |
|
| 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 |
0.35 |
|
| 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 |
0.453 |
|
| 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 |
0.522 |
|
| 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 |
0.801 |
|
| 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 |
0.758 |
|
| 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 |
0.409 |
|
| 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 |
0.796 |
|
| 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 |
0.662 |
|
| 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 |
0.377 |
|
| 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 |
0.379 |
|
| 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 |
0.5 |
|
| 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 |
0.718 |
|
| 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 |
0.663 |
|
| 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 |
0.371 |
|
| 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 |
0.799 |
|
| 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 |
0.353 |
|
| 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 |
0.524 |
|
| 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 |
0.74 |
|
| 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 |
0.487 |
|
| 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 |
0.616 |
|
| 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 |
0.337 |
|
| 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 |
0.42 |
|
| 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 |
0.684 |
|
| 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 |
0.537 |
|
| 2012 |
Brunger AT, Adams PD, Fromme P, Fromme R, Levitt M, Schröder GF. Improving the accuracy of macromolecular structure refinement at 7 Å resolution. Structure (London, England : 1993). 20: 957-66. PMID 22681901 DOI: 10.1016/J.Str.2012.04.020 |
0.563 |
|
| 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 |
0.548 |
|
| 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 |
0.392 |
|
| 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 |
0.666 |
|
| 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 |
0.799 |
|
| 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 |
0.734 |
|
| 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 |
0.503 |
|
| 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 |
0.582 |
|
| 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 |
0.352 |
|
| 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 |
0.459 |
|
| 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 |
0.732 |
|
| 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 |
0.805 |
|
| 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 |
0.393 |
|
| 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 |
0.767 |
|
| 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 |
0.791 |
|
| 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 |
0.374 |
|
| 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 |
0.657 |
|
| 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 |
0.476 |
|
| 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 |
0.58 |
|
| 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 |
0.547 |
|
| 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 |
0.326 |
|
| 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 |
0.548 |
|
| 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 |
0.476 |
|
| 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 |
0.568 |
|
| 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 |
0.507 |
|
| 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 |
0.721 |
|
| 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 |
0.543 |
|
| 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 |
0.511 |
|
| 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 |
0.507 |
|
| 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 |
0.553 |
|
| 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 |
0.453 |
|
| 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 |
0.5 |
|
| Show low-probability matches. |