☰

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, United States 
Area:
crystallography, cryo-EM, computational methods, structural biology
Website:
http://cci.lbl.gov/~paul/
Tree Info Similar researchers PubMed Report error

143/305 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
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 Ã… 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
Low-probability matches (unlikely to be authored by this person)
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  0.3
2014 Moriarty NW, Tronrud DE, Adams PD, Karplus PA. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. The Febs Journal. 281: 4061-71. PMID 24890778 DOI: 10.1111/febs.12860  0.299
2010 Afonine PV, Mustyakimov M, Grosse-Kunstleve RW, Moriarty NW, Langan P, Adams PD. Joint X-ray and neutron refinement with phenix.refine Acta Crystallographica Section D: Biological Crystallography. 66: 1153-1163. PMID 21041930 DOI: 10.1107/S0907444910026582  0.298
2019 Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, et al. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993). PMID 31780431 DOI: 10.1016/J.Str.2019.11.002  0.296
2009 Adams PD, Mustyakimov M, Afonine PV, Langan P. Generalized X-ray and neutron crystallographic analysis: More accurate and complete structures for biological macromolecules Acta Crystallographica Section D: Biological Crystallography. 65: 567-573. PMID 19465771 DOI: 10.1107/S0907444909011548  0.292
2013 Nwachukwu JC, Southern MR, Kiefer JR, Afonine PV, Adams PD, Terwilliger TC, Nettles KW. Improved crystallographic structures using extensive combinatorial refinement. Structure (London, England : 1993). 21: 1923-30. PMID 24076406 DOI: 10.1016/J.Str.2013.07.025  0.289
2021 van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure (London, England : 1993). PMID 33823127 DOI: 10.1016/j.str.2021.03.011  0.28
2012 Burnley BT, Afonine PV, Adams PD, Gros P. Modelling dynamics in protein crystal structures by ensemble refinement. Elife. 1: e00311. PMID 23251785 DOI: 10.7554/Elife.00311  0.276
2015 Sobolev OV, Afonine PV, Adams PD, Urzhumtsev A. Programming new geometry restraints: parallelity of atomic groups. Journal of Applied Crystallography. 48: 1130-1141. PMID 26306091 DOI: 10.1107/S1600576715010432  0.275
2022 Westbrook JD, Young JY, Shao C, Feng Z, Guranovic V, Lawson CL, Vallat B, Adams PD, Berrisford JM, Bricogne G, Diederichs K, Joosten RP, Keller P, Moriarty NW, Sobolev OV, et al. PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology. Journal of Molecular Biology. 167599. PMID 35460671 DOI: 10.1016/j.jmb.2022.167599  0.272
2011 Gabanyi MJ, Adams PD, 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, et al. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. Journal of Structural and Functional Genomics. 12: 45-54. PMID 21472436 DOI: 10.1007/S10969-011-9106-2  0.266
2007 Afonine PV, Grosse-Kunstleve RW, Adams PD, Lunin VY, Urzhumtsev A. On macromolecular refinement at subatomic resolution with interatomic scatterers Acta Crystallographica Section D: Biological Crystallography. 63: 1194-1197. PMID 18007035 DOI: 10.1107/S0907444907046148  0.266
2014 Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W. An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nature Communications. 5: 4808. PMID 25185801 DOI: 10.1038/Ncomms5808  0.265
2013 Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W. Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proceedings of the National Academy of Sciences of the United States of America. 110: 12301-6. PMID 23840063 DOI: 10.1073/Pnas.1309947110  0.265
2018 Kryshtafovych A, Adams PD, Lawson CL, Chiu W. Evaluation System and Web Infrastructure for the Second Cryo-EM Model Challenge. Journal of Structural Biology. PMID 30017700 DOI: 10.1016/J.Jsb.2018.07.006  0.263
2016 Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallographica. Section D, Structural Biology. 72: 1062-72. PMID 27599738 DOI: 10.1107/S2059798316012225  0.262
2017 Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W. Accurate model annotation of a near-atomic resolution cryo-EM map. Proceedings of the National Academy of Sciences of the United States of America. PMID 28270620 DOI: 10.1073/Pnas.1621152114  0.26
2018 Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nature Methods. 15: 905-908. PMID 30377346 DOI: 10.1038/s41592-018-0173-1  0.252
2009 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 PD, Carter LG, Minor W, et al. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research. 37: D365-8. PMID 19010965 DOI: 10.1093/Nar/Gkn790  0.251
2020 Sobolev OV, Afonine PV, Moriarty NW, Hekkelman ML, Joosten RP, Perrakis A, Adams PD. A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry. Structure (London, England : 1993). 28: 1249-1258.e2. PMID 32857966 DOI: 10.1016/j.str.2020.08.005  0.251
2023 Afonine PV, Adams PD, Urzhumtsev AG. Efficient structure-factor modeling for crystals with multiple components. Acta Crystallographica. Section a, Foundations and Advances. 79: 345-352. PMID 37338214 DOI: 10.1107/S205327332300356X  0.25
2018 Liebschner D, Afonine PV, Moriarty NW, Langan P, Adams PD. Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. Acta Crystallographica. Section D, Structural Biology. 74: 800-813. PMID 30082516 DOI: 10.1107/S2059798318004588  0.25
2009 Urzhumtsev A, Afonine PV, Adams PD. On the use of logarithmic scales for analysis of diffraction data Acta Crystallographica Section D: Biological Crystallography. 65: 1283-1291. PMID 19966414 DOI: 10.1107/S0907444909039638  0.249
2017 McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD. Reply to Kiser: Dioxygen binding in NOV1 crystal structures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28679635 DOI: 10.1073/Pnas.1708124114  0.245
2023 Afonine PV, Sobolev OV, Moriarty NW, Terwilliger TC, Adams PD. Overall protein structure quality assessment using hydrogen-bonding parameters. Acta Crystallographica. Section D, Structural Biology. PMID 37431759 DOI: 10.1107/S2059798323005077  0.244
2021 Terwilliger TC, Sobolev OV, Afonine PV, Adams PD, Ho CM, Li X, Zhou ZH. Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching. Acta Crystallographica. Section D, Structural Biology. 77: 457-462. PMID 33825706 DOI: 10.1107/S2059798321001765  0.242
2020 Liebschner D, Afonine PV, Moriarty NW, Adams PD. What are the current limits on determination of protonation state using neutron macromolecular crystallography? Methods in Enzymology. 634: 225-255. PMID 32093835 DOI: 10.1016/bs.mie.2020.01.008  0.239
2019 Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Cryo-EM map interpretation and protein model-building using iterative map segmentation. Protein Science : a Publication of the Protein Society. PMID 31599033 DOI: 10.1002/pro.3740  0.237
2022 Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. Structural plasticity enables evolution and innovation of RuBisCO assemblies. Science Advances. 8: eadc9440. PMID 36026446 DOI: 10.1126/sciadv.adc9440  0.235
2013 Urzhumtsev A, Afonine PV, Adams PD. from fundamentals to practice. Crystallography Reviews. 19: 230-270. PMID 25249713 DOI: 10.1080/0889311X.2013.835806  0.233
2012 Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. Journal of Structural and Functional Genomics. 13: 57-62. PMID 22527514 DOI: 10.1007/S10969-012-9133-7  0.23
2007 Oganesyan V, Adams PD, Jancarik J, Kim R, Kim SH. Structure of O67745_AQUAE, a hypothetical protein from Aquifex aeolicus. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 63: 369-74. PMID 17565173 DOI: 10.1107/S1744309107018945  0.229
2017 Welner DH, Tsai AY, DeGiovanni AM, Scheller HV, Adams PD. X-ray diffraction analysis and in vitro characterization of the UAM2 protein from Oryza sativa. Acta Crystallographica. Section F, Structural Biology Communications. 73: 241-245. PMID 28368284 DOI: 10.1107/S2053230X17004587  0.228
2005 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, ... ... Adams PD, et al. Structural genomics of minimal organisms and protein fold space. Journal of Structural and Functional Genomics. 6: 63-70. PMID 16211501 DOI: 10.1007/S10969-005-2651-9  0.226
2016 McAndrew RP, Sathitsuksanoh N, Mbughuni MM, Heins RA, Pereira JH, George A, Sale KL, Fox BG, Simmons BA, Adams PD. Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase. Proceedings of the National Academy of Sciences of the United States of America. PMID 27911781 DOI: 10.1073/Pnas.1608917113  0.223
2004 Kochva U, Leonov H, Arkin IT, Adams PD. Modeling membrane proteins utilizing information from silent amino acid substitutions Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 18428728  0.221
2016 Moriarty NW, Tronrud DE, Adams PD, Karplus PA. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream. Acta Crystallographica. Section D, Structural Biology. 72: 176-9. PMID 26894545 DOI: 10.1107/S2059798315022408  0.22
2004 Sauter NK, Grosse-Kunstleve RW, Adams PD. Robust indexing for automatic data collection. Journal of Applied Crystallography. 37: 399-409. PMID 20090869 DOI: 10.1107/S0021889804005874  0.217
2008 Langan P, Fisher Z, Kovalevsky A, Mustyakimov M, Sutcliffe Valone A, Unkefer C, Waltman MJ, Coates L, Adams PD, Afonine PV, Bennett B, Dealwis C, Schoenborn BP. Protein structures by spallation neutron crystallography. Journal of Synchrotron Radiation. 15: 215-8. PMID 18421142 DOI: 10.1107/S0909049508000824  0.214
2018 Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. Journal of Structural Biology. PMID 30063987 DOI: 10.1016/j.jsb.2018.07.016  0.213
2009 Pereira JH, Sapra R, Volponi JV, Kozina CL, Simmons B, Adams PD. Structure of endoglucanase Cel9A from the thermoacidophilic Alicyclobacillus acidocaldarius Acta Crystallographica Section D: Biological Crystallography. 65: 744-750. PMID 19622857 DOI: 10.1107/S0907444909012773  0.207
2017 Moriarty NW, Draizen EJ, Adams PD. An editor for the generation and customization of geometry restraints. Acta Crystallographica. Section D, Structural Biology. 73: 123-130. PMID 28177308 DOI: 10.1107/S2059798316016570  0.205
2015 Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS. Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles. Acta Crystallographica. Section D, Biological Crystallography. 71: 1657-67. PMID 26249347 DOI: 10.1107/S1399004715007415  0.205
2005 Kazantsev AV, Krivenko AA, Harrington DJ, Holbrook SR, Adams PD, Pace NR. Crystal structure of a bacterial ribonuclease P RNA. Proceedings of the National Academy of Sciences of the United States of America. 102: 13392-7. PMID 16157868 DOI: 10.1073/Pnas.0506662102  0.2
2010 Nishi K, Lee HJ, Park SY, Bae SJ, Lee SE, Adams PD, Rhee JH, Kim JS. Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6. Febs Letters. 584: 1097-102. PMID 20178784 DOI: 10.1016/j.febslet.2010.02.052  0.199
2010 Kohn JE, Afonine PV, Ruscio JZ, Adams PD, Head-Gordon T. Evidence of functional protein dynamics from X-ray crystallographic ensembles Plos Computational Biology. 6. PMID 20865158 DOI: 10.1371/Journal.Pcbi.1000911  0.199
2023 Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nature Plants. PMID 36849618 DOI: 10.1038/s41477-023-01358-4  0.197
2005 Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH. Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP. Journal of Molecular Biology. 354: 289-303. PMID 16242716 DOI: 10.1016/J.Jmb.2005.09.026  0.197
2017 Kohler AC, Mills MJ, Adams PD, Simmons BA, Sale KL. Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proceedings of the National Academy of Sciences of the United States of America. PMID 28373573 DOI: 10.1073/Pnas.1619263114  0.196
2010 Pereira JH, Chen Z, McAndrew RP, Sapra R, Chhabra SR, Sale KL, Simmons BA, Adams PD. Biochemical characterization and crystal structure of endoglucanase Cel5A from the hyperthermophilic Thermotoga maritima. Journal of Structural Biology. 172: 372-9. PMID 20599513 DOI: 10.1016/j.jsb.2010.06.018  0.196
2007 Hohn M, Tang G, Goodyear G, Baldwin PR, Huang Z, Penczek PA, Yang C, Glaeser RM, Adams PD, Ludtke SJ. SPARX, a new environment for Cryo-EM image processing Journal of Structural Biology. 157: 47-55. PMID 16931051 DOI: 10.1016/J.Jsb.2006.07.003  0.196
2005 Oganesyan V, Huang C, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH. Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 61: 640-6. PMID 16511117 DOI: 10.1107/S1744309105019780  0.19
2018 Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W. Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. Data in Brief. 20: 1629-1638. PMID 30263915 DOI: 10.1016/J.Dib.2018.08.214  0.188
2009 Pražnikar J, Afonine PV, Gunčar G, Adams PD, Turk D. Averaged kick maps: Less noise, more signal and probably less bias Acta Crystallographica Section D: Biological Crystallography. 65: 921-931. PMID 19690370 DOI: 10.1107/S0907444909021933  0.187
2017 Pereira JH, McAndrew RP, Sergeeva OA, Ralston CY, King JA, Adams PD. Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy. Scientific Reports. 7: 3673. PMID 28623285 DOI: 10.1038/S41598-017-03825-3  0.187
2018 Ellinghaus TL, Pereira JH, McAndrew RP, Welner DH, DeGiovanni AM, Guenther JM, Tran HM, Feldman T, Simmons BA, Sale KL, Adams PD. Engineering glycoside hydrolase stability by the introduction of zinc binding. Acta Crystallographica. Section D, Structural Biology. 74: 702-710. PMID 29968680 DOI: 10.1107/S2059798318006678  0.186
2020 Moriarty NW, Liebschner D, Tronrud DE, Adams PD. Arginine off-kilter: guanidinium is not as planar as restraints denote. Acta Crystallographica. Section D, Structural Biology. 76: 1159-1166. PMID 33263321 DOI: 10.1107/S2059798320013534  0.185
2005 Liu J, Lou Y, Yokota H, Adams PD, Kim R, Kim SH. Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters. The Journal of Biological Chemistry. 280: 15960-6. PMID 15716271 DOI: 10.1074/Jbc.M414117200  0.185
2015 Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Acta Crystallographica. Section D, Biological Crystallography. 71: 1668-83. PMID 26249348 DOI: 10.1107/S1399004715011426  0.184
2017 Pereira JH, McAndrew RP, Tomaleri GP, Adams PD. Berkeley Screen: a set of 96 solutions for general macromolecular crystallization. Journal of Applied Crystallography. 50: 1352-1358. PMID 29021733 DOI: 10.1107/S1600576717011347  0.183
2016 Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams PD. Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing. Acta Crystallographica. Section D, Structural Biology. 72: 346-58. PMID 26960122 DOI: 10.1107/S2059798315019269  0.183
2005 Oganesyan V, Oganesyan N, Adams PD, Jancarik J, Yokota HA, Kim R, Kim SH. Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus. Journal of Bacteriology. 187: 4238-44. PMID 15937186 DOI: 10.1128/Jb.187.12.4238-4244.2005  0.182
2003 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 PD, et al. X-ray crystallographic and kinetic studies of human sorbitol dehydrogenase. Structure (London, England : 1993). 11: 1071-85. PMID 12962626 DOI: 10.1016/s0969-2126(03)00167-9  0.18
2015 Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman CA, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural basis of stereospecificity in the bacterial enzymatic cleavage of β-aryl ether bonds in lignin. The Journal of Biological Chemistry. PMID 26637355 DOI: 10.1074/Jbc.M115.694307  0.178
2009 Urzhumtseva L, Afonine PV, Adams PD, Urzhumtsev A. Crystallographic model quality at a glance Acta Crystallographica Section D: Biological Crystallography. 65: 297-300. PMID 19237753 DOI: 10.1107/S0907444908044296  0.177
2014 Wall ME, Adams PD, Fraser JS, Sauter NK. Diffuse X-ray scattering to model protein motions. Structure (London, England : 1993). 22: 182-4. PMID 24507780 DOI: 10.1016/J.Str.2014.01.002  0.176
2021 Wang X, Pereira JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee TS. Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450. Metabolic Engineering. PMID 33482331 DOI: 10.1016/j.ymben.2021.01.004  0.176
2006 Adams PD, Oswald RE. Solution structure of an oncogenic mutant of Cdc42Hs. Biochemistry. 45: 2577-83. PMID 16489751 DOI: 10.1021/bi051686g  0.175
2020 Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. Novel bacterial clade reveals origin of form I Rubisco. Nature Plants. PMID 32868887 DOI: 10.1038/S41477-020-00762-4  0.173
2014 Urzhumtsev A, Afonine PV, Lunin VY, Terwilliger TC, Adams PD. Metrics for comparison of crystallographic maps. Acta Crystallographica. Section D, Biological Crystallography. 70: 2593-606. PMID 25286844 DOI: 10.1107/S1399004714016289  0.172
2019 Moriarty NW, Adams PD. Iron-sulfur clusters have no right angles. Acta Crystallographica. Section D, Structural Biology. 75: 16-20. PMID 30644841 DOI: 10.1107/S205979831801519X  0.171
2003 Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR. High-resolution structure of RNase P protein from Thermotoga maritima. Proceedings of the National Academy of Sciences of the United States of America. 100: 7497-502. PMID 12799461 DOI: 10.1073/Pnas.0932597100  0.17
2010 Pereira JH, Ralston CY, Douglas NR, Meyer D, Knee KM, Goulet DR, King JA, Frydman J, Adams PD. Crystal structures of a group II chaperonin reveal the open and closed states associated with the protein folding cycle. The Journal of Biological Chemistry. 285: 27958-66. PMID 20573955 DOI: 10.1074/Jbc.M110.125344  0.169
2005 Liu J, Huang C, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, Kim SH. Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. Journal of Molecular Biology. 350: 987-96. PMID 15979091 DOI: 10.1016/J.Jmb.2005.04.021  0.168
2013 Parsons HT, Weinberg CS, Macdonald LJ, Adams PD, Petzold CJ, Strabala TJ, Wagner A, Heazlewood JL. Golgi enrichment and proteomic analysis of developing Pinus radiata xylem by free-flow electrophoresis. Plos One. 8: e84669. PMID 24416096 DOI: 10.1371/Journal.Pone.0084669  0.166
2010 Schmidt M, Perera P, Schwartzberg AM, Adams PD, Schuck PJ. Label-free in situ imaging of lignification in plant cell walls. Journal of Visualized Experiments : Jove. PMID 21085100 DOI: 10.3791/2064  0.164
2009 Moriarty NW, Grosse-Kunstleve RW, Adams PD. Electronic ligand builder and optimization workbench (eLBOW): A tool for ligand coordinate and restraint generation Acta Crystallographica Section D: Biological Crystallography. 65: 1074-1080. PMID 19770504 DOI: 10.1107/S0907444909029436  0.163
2015 González Fernández-Niño SM, Smith-Moritz AM, Chan LJ, Adams PD, Heazlewood JL, Petzold CJ. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Frontiers in Bioengineering and Biotechnology. 3: 44. PMID 25883932 DOI: 10.3389/Fbioe.2015.00044  0.162
2012 Perera PN, Schmidt M, Chiang VL, Schuck PJ, Adams PD. Raman-spectroscopy-based noninvasive microanalysis of native lignin structure. Analytical and Bioanalytical Chemistry. 402: 983-7. PMID 22071606 DOI: 10.1007/S00216-011-5518-X  0.16
2016 Terwilliger TC, Bunkóczi G, Hung LW, Zwart PH, Smith JL, Akey DL, Adams PD. Can I solve my structure by SAD phasing? Planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. Acta Crystallographica. Section D, Structural Biology. 72: 359-74. PMID 26960123 DOI: 10.1107/S2059798315019403  0.16
2006 Terwilliger TC, Klei H, Adams PD, Moriarty NW, Cohn JD. Automated ligand fitting by core-fragment fitting and extension into density Acta Crystallographica Section D: Biological Crystallography. 62: 915-922. PMID 16855309 DOI: 10.1107/S0907444906017161  0.159
2014 Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proceedings of the National Academy of Sciences of the United States of America. 111: 17887-92. PMID 25453071 DOI: 10.1073/Pnas.1416744111  0.158
2017 Greber BJ, Nguyen THD, Fang J, Afonine PV, Adams PD, Nogales E. The cryo-electron microscopy structure of human transcription factor IIH. Nature. PMID 28902838 DOI: 10.1038/Nature23903  0.155
2013 Chang C, Sustarich J, Bharadwaj R, Chandrasekaran A, Adams PD, Singh AK. Droplet-based microfluidic platform for heterogeneous enzymatic assays Lab On a Chip - Miniaturisation For Chemistry and Biology. 13: 1817-1822. PMID 23507976 DOI: 10.1039/C3Lc41418C  0.155
2016 Morris KM, Henderson R, Suresh Kumar TK, Heyes CD, Adams PD. Intrinsic GTP Hydrolysis is Observed For a Switch 1 Variant of Cdc42 in the Presence of a Specific GTPase Inhibitor. Small Gtpases. 0. PMID 26828437 DOI: 10.1080/21541248.2015.1123797  0.155
2007 Terwilliger TC, Adams PD, Moriarty NW, Cohn JD. Ligand identification using electron-density map correlations. Acta Crystallographica. Section D, Biological Crystallography. 63: 101-7. PMID 17164532 DOI: 10.1107/S0907444906046233  0.155
2023 Dai J, Wilhelm KB, Bischoff AJ, Pereira JH, Dedeo MT, García-Almedina DM, Adams PD, Groves JT, Francis MB. A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins. Small (Weinheim An Der Bergstrasse, Germany). e2207805. PMID 36811150 DOI: 10.1002/smll.202207805  0.154
2010 Bharadwaj R, Chen Z, Datta S, Holmes BM, Sapra R, Simmons BA, Adams PD, Singh AK. Microfluidic glycosyl hydrolase screening for biomass-to-biofuel conversion. Analytical Chemistry. 82: 9513-20. PMID 20964411 DOI: 10.1021/Ac102243F  0.154
2017 Welner DH, Shin D, Tomaleri GP, DeGiovanni AM, Tsai AY, Tran HM, Hansen SF, Green DT, Scheller HV, Adams PD. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes. Plos One. 12: e0177591. PMID 28598995 DOI: 10.1371/Journal.Pone.0177591  0.154
2016 Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-aryl Ether Cleavage Pathway from Sphingobium sp SYK-6. The Journal of Biological Chemistry. PMID 26940872 DOI: 10.1074/Jbc.M115.700427  0.152
2018 Afonine PV, Adams PD, Urzhumtsev A. From deep TLS validation to ensembles of atomic models built from elemental motions. II. Analysis of TLS refinement results by explicit interpretation. Acta Crystallographica. Section D, Structural Biology. 74: 621-631. PMID 29968672 DOI: 10.1107/S2059798318005764  0.151
2012 Pereira JH, Ralston CY, Douglas NR, Kumar R, Lopez T, McAndrew RP, Knee KM, King JA, Frydman J, Adams PD. Mechanism of nucleotide sensing in group II chaperonins. The Embo Journal. 31: 731-40. PMID 22193720 DOI: 10.1038/Emboj.2011.468  0.15
2018 Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, ... ... Adams PD, et al. Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature. PMID 30405241 DOI: 10.1038/S41586-018-0681-2  0.148
2005 Kim JS, DeGiovanni A, Jancarik J, Adams PD, Yokota H, Kim R, Kim SH. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proceedings of the National Academy of Sciences of the United States of America. 102: 3248-53. PMID 15728358 DOI: 10.1073/Pnas.0409851102  0.147
2005 Afonine PV, Grosse-Kunstleve RW, Adams PD. A robust bulk-solvent correction and anisotropic scaling procedure Acta Crystallographica Section D: Biological Crystallography. 61: 850-855. PMID 15983406 DOI: 10.1107/S0907444905007894  0.145
2009 Afonine PV, Grosse-Kunstleve RW, Urzhumtsev A, Adams PD. Automatic multiple-zone rigid-body refinement with a large convergence radius. Journal of Applied Crystallography. 42: 607-615. PMID 19649324 DOI: 10.1107/S0021889809023528  0.144
2007 Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD. Surprises and pitfalls arising from (pseudo)symmetry Acta Crystallographica Section D: Biological Crystallography. 64: 99-107. PMID 18094473 DOI: 10.1107/S090744490705531X  0.144
2012 Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ. Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. Bmc Biotechnology. 12: 38. PMID 22759983 DOI: 10.1186/1472-6750-12-38  0.144
2015 Petzold CJ, Chan LJ, Nhan M, Adams PD. Analytics for Metabolic Engineering. Frontiers in Bioengineering and Biotechnology. 3: 135. PMID 26442249 DOI: 10.3389/Fbioe.2015.00135  0.143
2014 McAndrew R, Pruitt RN, Kamita SG, Pereira JH, Majumdar D, Hammock BD, Adams PD, Ronald PC. Structure of the OsSERK2 leucine-rich repeat extracellular domain. Acta Crystallographica. Section D, Biological Crystallography. 70: 3080-6. PMID 25372696 DOI: 10.1107/S1399004714021178  0.142
2015 Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. Acta Crystallographica. Section D, Biological Crystallography. 71: 646-66. PMID 25760612 DOI: 10.1107/S1399004714028132  0.139
2020 Liebschner D, Afonine PV, Urzhumtsev AG, Adams PD. Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix. Methods in Enzymology. 634: 177-199. PMID 32093832 DOI: 10.1016/bs.mie.2020.01.007  0.137
2016 Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum. Acta Crystallographica. Section D, Structural Biology. 72: 1073-1075. PMID 27599739 DOI: 10.1107/S2059798316013048  0.135
2010 Chandrasekaran A, Bharadwaj R, Park JI, Sapra R, Adams PD, Singh AK. A microscale platform for integrated cell-free expression and activity screening of cellulases Journal of Proteome Research. 9: 5677-5683. PMID 20735086 DOI: 10.1021/pr1003938  0.135
2018 Terwilliger TC, Sobolev OV, Afonine PV, Adams PD. Automated map sharpening by maximization of detail and connectivity. Acta Crystallographica. Section D, Structural Biology. 74: 545-559. PMID 29872005 DOI: 10.1107/S2059798318004655  0.135
2011 Chandrashekar R, Salem O, Krizova H, McFeeters R, Adams PD. A switch I mutant of Cdc42 exhibits less conformational freedom Biochemistry. 50: 6196-6207. PMID 21667996 DOI: 10.1021/Bi2004284  0.134
2008 Rajalingam D, Kathir KM, Ananthamurthy K, Adams PD, Kumar TK. A method for the prevention of thrombin-induced degradation of recombinant proteins. Analytical Biochemistry. 375: 361-3. PMID 18279654 DOI: 10.1016/j.ab.2008.01.014  0.134
2023 Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, ... ... Adams PD, et al. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nature Communications. 14: 1733. PMID 36977673 DOI: 10.1038/s41467-023-37254-w  0.133
2018 Hsu TM, Welner DH, Russ ZN, Cervantes B, Prathuri RL, Adams PD, Dueber JE. Employing a biochemical protecting group for a sustainable indigo dyeing strategy. Nature Chemical Biology. PMID 29309053 DOI: 10.1038/Nchembio.2552  0.133
2011 Bharadwaj R, Wong A, Knierim B, Singh S, Holmes BM, Auer M, Simmons BA, Adams PD, Singh AK. High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresource Technology. 102: 1329-37. PMID 20884206 DOI: 10.1016/j.biortech.2010.08.108  0.131
2010 Bruning JB, Parent AA, Gil G, Zhao M, Nowak J, Pace MC, Smith CL, Afonine PV, Adams PD, Katzenellenbogen JA, Nettles KW. Coupling of receptor conformation and ligand orientation determine graded activity. Nature Chemical Biology. 6: 837-43. PMID 20924370 DOI: 10.1038/Nchembio.451  0.129
2015 Schwessinger B, Li X, Ellinghaus TL, Chan LJ, Wei T, Joe A, Thomas N, Pruitt R, Adams PD, Chern MS, Petzold CJ, Liu CC, Ronald PC. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 26611838 DOI: 10.1039/C5Ib00232J  0.129
2023 Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, ... ... Adams PD, et al. Structural evidence for intermediates during O formation in photosystem II. Nature. PMID 37138085 DOI: 10.1038/s41586-023-06038-z  0.129
2013 Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnology For Biofuels. 6: 93. PMID 23819686 DOI: 10.1186/1754-6834-6-93  0.129
2004 Adams PD, Loh AP, Oswald RE. Backbone dynamics of an oncogenic mutant of Cdc42Hs shows increased flexibility at the nucleotide-binding site. Biochemistry. 43: 9968-77. PMID 15287724 DOI: 10.1021/bi0490901  0.128
2013 Chen Z, Pereira JH, Liu H, Tran HM, Hsu NS, Dibble D, Singh S, Adams PD, 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. 8: e79725. PMID 24244549 DOI: 10.1371/Journal.Pone.0079725  0.126
2022 Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Garcia Martin H, Singh AK. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. Microsystems & Nanoengineering. 8: 31. PMID 35359611 DOI: 10.1038/s41378-022-00357-3  0.125
2011 Gildea RJ, Bourhis LJ, Dolomanov OV, Grosse-Kunstleve RW, Puschmann H, Adams PD, Howard JA. iotbx.cif: a comprehensive CIF toolbox. Journal of Applied Crystallography. 44: 1259-1263. PMID 22199401 DOI: 10.1107/S0021889811041161  0.123
2015 Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, et al. NMR Exchange Format: a unified and open standard for representation of NMR restraint data. Nature Structural & Molecular Biology. 22: 433-4. PMID 26036565 DOI: 10.1038/Nsmb.3041  0.123
2021 Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, ... ... Adams PD, et al. Structural dynamics in the water and proton channels of photosystem II during the S to S transition. Nature Communications. 12: 6531. PMID 34764256 DOI: 10.1038/s41467-021-26781-z  0.121
2024 Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, et al. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metabolic Engineering. PMID 38369052 DOI: 10.1016/j.ymben.2024.02.004  0.12
2024 Pham LTM, Deng K, Choudhary H, Northen TR, Singer SW, Adams PD, Simmons BA, Sale KL. An Engineered Laccase from Accelerates Lignocellulose Degradation. Biomolecules. 14. PMID 38540744 DOI: 10.3390/biom14030324  0.12
2024 Afonine PV, Adams PD, Sobolev OV, Urzhumtsev AG. Accounting for nonuniformity of bulk-solvent: A mosaic model. Protein Science : a Publication of the Protein Society. 33: e4909. PMID 38358136 DOI: 10.1002/pro.4909  0.12
2022 Chen Y, Kaplan Lease N, Gin JW, Ogorzalek TL, Adams PD, Hillson NJ, Petzold CJ. Modular automated bottom-up proteomic sample preparation for high-throughput applications. Plos One. 17: e0264467. PMID 35213656 DOI: 10.1371/journal.pone.0264467  0.12
2017 Amaike Campen S, Lynn J, Sibert SJ, Srikrishnan S, Phatale P, Feldman T, Guenther JM, Hiras J, Tran YTA, Singer SW, Adams PD, Sale KL, Simmons BA, Baker SE, Magnuson JK, et al. Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger. Plos One. 12: e0189604. PMID 29281693 DOI: 10.1371/Journal.Pone.0189604  0.117
2012 McClendon SD, Batth T, Petzold CJ, Adams PD, Simmons BA, Singer SW. Thermoascus aurantiacus is a promising source of enzymes for biomass deconstruction under thermophilic conditions. Biotechnology For Biofuels. 5: 54. PMID 22839529 DOI: 10.1186/1754-6834-5-54  0.117
2011 Perera PN, Schmidt M, Schuck PJ, Adams PD. Blind image analysis for the compositional and structural characterization of plant cell walls. Analytica Chimica Acta. 702: 172-7. PMID 21839194 DOI: 10.1016/J.Aca.2011.06.021  0.116
2024 Bhowmick A, Hussein R, Bogacz I, Simon PS, Ibrahim M, Chatterjee R, Doyle MD, Cheah MH, Fransson T, Chernev P, Kim IS, Makita H, Dasgupta M, Kaminsky CJ, Zhang M, ... ... Adams PD, et al. Author Correction: Structural evidence for intermediates during O formation in photosystem II. Nature. PMID 38291188 DOI: 10.1038/s41586-024-07099-4  0.115
2022 Macdonald SS, Pereira JH, Liu F, Tegl G, DeGiovanni A, Wardman JF, Deutsch S, Yoshikuni Y, Adams PD, Withers SG. A Synthetic Gene Library Yields a Previously Unknown Glycoside Phosphorylase That Degrades and Assembles Poly-β-1,3-GlcNAc, Completing the Suite of β-Linked GlcNAc Polysaccharides. Acs Central Science. 8: 430-440. PMID 35505869 DOI: 10.1021/acscentsci.1c01570  0.115
2002 Liu B, Thalji RK, Adams PD, Fronczek FR, McLaughlin ML, Barkley MD. Fluorescence of cis-1-amino-2-(3-indolyl)cyclohexane-1-carboxylic acid: a single tryptophan chi(1) rotamer model. Journal of the American Chemical Society. 124: 13329-38. PMID 12405862 DOI: 10.1021/Ja016542D  0.115
2014 Pereira JH, Petchprayoon C, Hoepker AC, Moriarty NW, Fink SJ, Cecere G, Paterson I, Adams PD, Marriott G. Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues. Chemmedchem. 9: 2286-93. PMID 25047814 DOI: 10.1002/Cmdc.201402150  0.114
2021 Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS. Engineering Saccharomyces cerevisiae for isoprenol production. Metabolic Engineering. PMID 33581331 DOI: 10.1016/j.ymben.2021.02.002  0.111
2006 Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science (New York, N.Y.). 311: 195-8. PMID 16410517 DOI: 10.1126/Science.1121638  0.111
2014 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 PD, et al. The plant glycosyltransferase clone collection for functional genomics. The Plant Journal : For Cell and Molecular Biology. 79: 517-29. PMID 24905498 DOI: 10.1111/Tpj.12577  0.108
2017 Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, et al. A bacterial pioneer produces cellulase complexes that persist through community succession. Nature Microbiology. PMID 29109478 DOI: 10.1038/S41564-017-0052-Z  0.108
2015 Shih SC, Gach PC, Sustarich J, Simmons BA, Adams PD, Singh S, Singh AK. A droplet-to-digital (D2D) microfluidic device for single cell assays. Lab On a Chip. 15: 225-36. PMID 25354549 DOI: 10.1039/C4Lc00794H  0.101
2018 Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Jungle Express is a versatile repressor system for tight transcriptional control. Nature Communications. 9: 3617. PMID 30190458 DOI: 10.1038/S41467-018-05857-3  0.098
2002 Adams PD, Chen Y, Ma K, Zagorski MG, Sönnichsen FD, McLaughlin ML, Barkley MD. Intramolecular quenching of tryptophan fluorescence by the peptide bond in cyclic hexapeptides. Journal of the American Chemical Society. 124: 9278-86. PMID 12149035 DOI: 10.1021/Ja0167710  0.098
2023 Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in M2. Applied and Environmental Microbiology. e0085223. PMID 37724856 DOI: 10.1128/aem.00852-23  0.096
2019 Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW. Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids. Biotechnology and Bioengineering. PMID 30982958 DOI: 10.1002/Bit.26995  0.095
2013 Chandrashekar R, Adams PD. Prospective Development of Small Molecule Targets to Oncogenic Ras Proteins. Open Journal of Biophysics. 3: 207-211. PMID 25392746 DOI: 10.4236/ojbiphy.2013.34025  0.092
2004 Kwon YD, Nagy I, Adams PD, 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. Journal of Molecular Biology. 335: 233-45. PMID 14659753 DOI: 10.1016/J.Jmb.2003.08.029  0.091
2011 Grosse-Kunstleve RW, Wong B, Mustyakimov M, Adams PD. Exact direct-space asymmetric units for the 230 crystallographic space groups Acta Crystallographica Section a: Foundations of Crystallography. 67: 269-275. PMID 21487185 DOI: 10.1107/S0108767311007008  0.087
2018 Ruegg TL, Pereira JH, Chen JC, DeGiovanni A, Novichkov P, Mutalik VK, Tomaleri GP, Singer SW, Hillson NJ, Simmons BA, Adams PD, Thelen MP. Author Correction: Jungle Express is a versatile repressor system for tight transcriptional control. Nature Communications. 9: 4596. PMID 30375402 DOI: 10.1038/S41467-018-07111-2  0.087
2013 Chandrasekaran A, Deng K, Koh CY, Takasuka T, Bergeman LF, Fox BG, Adams PD, Singh AK. A universal flow cytometry assay for screening carbohydrate-active enzymes using glycan microspheres Chemical Communications. 49: 5441-5443. PMID 23536035 DOI: 10.1039/C3Cc39155H  0.083
2010 Achyuthan KE, Achyuthan AM, Adams PD, Dirk SM, Harper JC, Simmons BA, Singh AK. Supramolecular self-assembled chaos: polyphenolic lignin's barrier to cost-effective lignocellulosic biofuels. Molecules (Basel, Switzerland). 15: 8641-88. PMID 21116223 DOI: 10.3390/molecules15118641  0.082
2022 Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Scientific Reports. 12: 12197. PMID 35842458 DOI: 10.1038/s41598-022-15930-z  0.081
2014 Rennie EA, Ebert B, Miles GP, Cahoon RE, Christiansen KM, Stonebloom S, Khatab H, Twell D, Petzold CJ, Adams PD, Dupree P, Heazlewood JL, Cahoon EB, Scheller HV. Identification of a sphingolipid α-glucuronosyltransferase that is essential for pollen function in Arabidopsis. The Plant Cell. 26: 3314-25. PMID 25122154 DOI: 10.1105/Tpc.114.129171  0.08
2010 Liu H, Pereira JH, Adams PD, Sapra R, Simmons BA, Sale KL. Molecular simulations provide new insights into the role of the accessory immunoglobulin-like domain of Cel9A. Febs Letters. 584: 3431-5. PMID 20609364 DOI: 10.1016/J.Febslet.2010.06.041  0.079
2010 Schmidt M, Schwartzberg AM, Carroll A, Chaibang A, Adams PD, Schuck PJ. Raman imaging of cell wall polymers in Arabidopsis thaliana. Biochemical and Biophysical Research Communications. 395: 521-3. PMID 20394731 DOI: 10.1016/J.Bbrc.2010.04.055  0.077
2015 Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJ, Adams PD, Petzold CJ, Pauly M, Willats WG, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. The Plant Cell. 27: 1218-27. PMID 25804536 DOI: 10.1105/Tpc.114.133827  0.076
2021 Ibrahim M, Moriarty NW, Kern J, Holton JM, Brewster AS, Bhowmick A, Bergmann U, Zouni A, Messinger J, Yachandra VK, Yano J, Dobbek H, Sauter NK, Adams PD. Reply to Wang et al.: Clear evidence of binding of Ox to the oxygen-evolving complex of photosystem II is best observed in the omit map. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34117122 DOI: 10.1073/pnas.2102342118  0.076
2013 Chiniquy D, Varanasi P, Oh T, Harholt J, Katnelson J, Singh S, Auer M, Simmons B, Adams PD, Scheller HV, Ronald PC. Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Frontiers in Plant Science. 4: 83. PMID 23596448 DOI: 10.3389/fpls.2013.00083  0.073
2012 Grosse-Kunstleve RW, Terwilliger TC, Sauter NK, Adams PD. Automatic Fortran to C++ conversion with FABLE. Source Code For Biology and Medicine. 7: 5. PMID 22640868 DOI: 10.1186/1751-0473-7-5  0.072
2007 Adams PD, Oswald RE. NMR assignment of Cdc42(T35A), an active Switch I mutant of Cdc42. Biomolecular Nmr Assignments. 1: 225-7. PMID 19636871 DOI: 10.1007/s12104-007-9062-8  0.072
2009 Achyuthan KE, Adams PD, Simmons BA, Singh AK. Spectroscopic analyses of the biofuels-critical phytochemical coniferyl alcohol and its enzyme-catalyzed oxidation products Molecules. 14: 4758-4778. PMID 19935474 DOI: 10.3390/molecules14114758  0.071
2014 Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK. Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Lab On a Chip. 14: 4533-9. PMID 25270338 DOI: 10.1039/C4Lc00823E  0.064
2014 Dougherty MJ, Tran HM, Stavila V, Knierim B, George A, Auer M, Adams PD, Hadi MZ. Cellulosic biomass pretreatment and sugar yields as a function of biomass particle size. Plos One. 9: e100836. PMID 24971883 DOI: 10.1371/journal.pone.0100836  0.057
2012 Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons BA, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresource Technology. 126: 156-61. PMID 23073103 DOI: 10.1016/j.biortech.2012.08.070  0.055
2013 Varanasi P, Singh P, Auer M, Adams PD, Simmons BA, Singh S. Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnology For Biofuels. 6: 14. PMID 23356589 DOI: 10.1186/1754-6834-6-14  0.046
2010 Achyuthan KE, Adams PD, Datta S, Simmons BA, Singh AK. Hitherto unrecognized fluorescence properties of coniferyl alcohol. Molecules (Basel, Switzerland). 15: 1645-67. PMID 20336005 DOI: 10.3390/Molecules15031645  0.043
2022 Adams PD, Muhoza DJ. Targeting K-Ras Mutations Show Promise Towards Ending Ras's "Undruggable" Era. Protein and Peptide Letters. PMID 36200189 DOI: 10.2174/0929866529666221003124202  0.039
Hide low-probability matches.