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Items: 1 to 50 of 119

1.

An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering.

Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS.

Elife. 2018 Jun 7;7. pii: e36307. doi: 10.7554/eLife.36307.

2.

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

Wang WJ, He HS, Thompson FR 3rd, Spetich MA, Fraser JS.

Sci Total Environ. 2018 Sep 1;634:1214-1221. doi: 10.1016/j.scitotenv.2018.03.353. Epub 2018 Apr 18.

PMID:
29710627
3.

Rescue of conformational dynamics in enzyme catalysis by directed evolution.

Otten R, Liu L, Kenner LR, Clarkson MW, Mavor D, Tawfik DS, Kern D, Fraser JS.

Nat Commun. 2018 Apr 3;9(1):1314. doi: 10.1038/s41467-018-03562-9.

4.

Bringing diffuse X-ray scattering into focus.

Wall ME, Wolff AM, Fraser JS.

Curr Opin Struct Biol. 2018 Feb 15;50:109-116. doi: 10.1016/j.sbi.2018.01.009. [Epub ahead of print] Review.

5.

XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.

Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13357-13362. doi: 10.1073/pnas.1705624114. Epub 2017 Aug 23.

6.

Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.

Acker TM, Gable JE, Bohn MF, Jaishankar P, Thompson MC, Fraser JS, Renslo AR, Craik CS.

J Am Chem Soc. 2017 Aug 30;139(34):11650-11653. doi: 10.1021/jacs.7b04030. Epub 2017 Aug 17.

PMID:
28759216
7.

Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling.

Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP.

ACS Cent Sci. 2017 Jun 28;3(6):570-579. doi: 10.1021/acscentsci.7b00142. Epub 2017 Jun 9.

8.

Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.

Biel JT, Thompson MC, Cunningham CN, Corn JE, Fraser JS.

Structure. 2017 May 2;25(5):739-749.e3. doi: 10.1016/j.str.2017.03.009. Epub 2017 Apr 13.

9.

Future forest aboveground carbon dynamics in the central United States: the importance of forest demographic processes.

Jin W, He HS, Thompson FR 3rd, Wang WJ, Fraser JS, Shifley SR, Hanberry BB, Dijak WD.

Sci Rep. 2017 Feb 6;7:41821. doi: 10.1038/srep41821.

10.

Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization.

Adolph MB, Ara A, Feng Y, Wittkopp CJ, Emerman M, Fraser JS, Chelico L.

Nucleic Acids Res. 2017 Apr 7;45(6):3378-3394. doi: 10.1093/nar/gkx066.

11.

Conformational variation of proteins at room temperature is not dominated by radiation damage.

Russi S, González A, Kenner LR, Keedy DA, Fraser JS, van den Bedem H.

J Synchrotron Radiat. 2017 Jan 1;24(Pt 1):73-82. doi: 10.1107/S1600577516017343. Epub 2017 Jan 1.

12.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F.

Elife. 2016 Sep 26;5. pii: e17219. doi: 10.7554/eLife.17219.

13.

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD.

Acta Crystallogr D Struct Biol. 2016 Sep 1;72(Pt 9):1073-1075. Epub 2016 Aug 31.

14.

SCIENTIFIC COMMUNITY. Preprints for the life sciences.

Berg JM, Bhalla N, Bourne PE, Chalfie M, Drubin DG, Fraser JS, Greider CW, Hendricks M, Jones C, Kiley R, King S, Kirschner MW, Krumholz HM, Lehmann R, Leptin M, Pulverer B, Rosenzweig B, Spiro JE, Stebbins M, Strasser C, Swaminathan S, Turner P, Vale RD, VijayRaghavan K, Wolberger C.

Science. 2016 May 20;352(6288):899-901. doi: 10.1126/science.aaf9133. No abstract available.

PMID:
27199406
15.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.

Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS.

Elife. 2016 Apr 25;5. pii: e15802. doi: 10.7554/eLife.15802.

16.

Measuring and modeling diffuse scattering in protein X-ray crystallography.

Van Benschoten AH, Liu L, Gonzalez A, Brewster AS, Sauter NK, Fraser JS, Wall ME.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4069-74. doi: 10.1073/pnas.1524048113. Epub 2016 Mar 28.

17.

Data publication with the structural biology data grid supports live analysis.

Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P.

Nat Commun. 2016 Mar 7;7:10882. doi: 10.1038/ncomms10882.

18.

High-density grids for efficient data collection from multiple crystals.

Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE.

Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):2-11. doi: 10.1107/S2059798315020847. Epub 2016 Jan 1.

19.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A.

J Mol Biol. 2016 Feb 22;428(4):709-719. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5.

20.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction.

Thomaston JL, Alfonso-Prieto M, Woldeyes RA, Fraser JS, Klein ML, Fiorin G, DeGrado WF.

Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):14260-5. doi: 10.1073/pnas.1518493112. Epub 2015 Nov 2. Erratum in: Proc Natl Acad Sci U S A. 2016 May 3;113(18):E2548.

21.

Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

Keedy DA, Fraser JS, van den Bedem H.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004507. doi: 10.1371/journal.pcbi.1004507. eCollection 2015 Oct.

22.

Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography.

Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS.

Elife. 2015 Sep 30;4. pii: e07574. doi: 10.7554/eLife.07574.

23.

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS.

Nat Methods. 2015 Oct;12(10):943-6. doi: 10.1038/nmeth.3541. Epub 2015 Aug 17.

24.

From deep TLS validation to ensembles of atomic models built from elemental motions.

Urzhumtsev A, Afonine PV, Van Benschoten AH, Fraser JS, Adams PD.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1668-83. doi: 10.1107/S1399004715011426. Epub 2015 Jul 28. Erratum in: Acta Crystallogr D Struct Biol. 2016 Sep;72(Pt 9):1073-5.

25.

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles.

Van Benschoten AH, Afonine PV, Terwilliger TC, Wall ME, Jackson CJ, Sauter NK, Adams PD, Urzhumtsev A, Fraser JS.

Acta Crystallogr D Biol Crystallogr. 2015 Aug;71(Pt 8):1657-67. doi: 10.1107/S1399004715007415. Epub 2015 Jul 28.

26.

One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites.

Fischer M, Shoichet BK, Fraser JS.

Chembiochem. 2015 Jul 27;16(11):1560-4. doi: 10.1002/cbic.201500196. Epub 2015 Jun 15.

27.

Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

Dellus-Gur E, Elias M, Caselli E, Prati F, Salverda ML, de Visser JA, Fraser JS, Tawfik DS.

J Mol Biol. 2015 Jul 17;427(14):2396-409. doi: 10.1016/j.jmb.2015.05.011. Epub 2015 May 22.

28.

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

Kane JR, Stanley DJ, Hultquist JF, Johnson JR, Mietrach N, Binning JM, Jónsson SR, Barelier S, Newton BW, Johnson TL, Franks-Skiba KE, Li M, Brown WL, Gunnarsson HI, Adalbjornsdóttir A, Fraser JS, Harris RS, Andrésdóttir V, Gross JD, Krogan NJ.

Cell Rep. 2015 May 26;11(8):1236-50. doi: 10.1016/j.celrep.2015.04.038. Epub 2015 May 14.

29.

Integrative, dynamic structural biology at atomic resolution--it's about time.

van den Bedem H, Fraser JS.

Nat Methods. 2015 Apr;12(4):307-18. doi: 10.1038/nmeth.3324. Review.

30.

Treatment Efficacy of Integrative Family and Systems Treatment (I-FAST) With and Without Consultation: The Role of Model Training in the Sustainability of Evidence-Based Family Treatments.

Lee MY, Hsu KS, Liu C, Greene GJ, Fraser JS, Grove D, Solovey A, Edwards SG, Scott P.

Adm Policy Ment Health. 2016 Jul;43(4):579-91. doi: 10.1007/s10488-015-0644-y.

PMID:
25813342
31.

Keep on moving: discovering and perturbing the conformational dynamics of enzymes.

Bhabha G, Biel JT, Fraser JS.

Acc Chem Res. 2015 Feb 17;48(2):423-30. doi: 10.1021/ar5003158. Epub 2014 Dec 24. Review.

32.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering.

Wall ME, Van Benschoten AH, Sauter NK, Adams PD, Fraser JS, Terwilliger TC.

Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):17887-92. doi: 10.1073/pnas.1416744111. Epub 2014 Dec 1.

33.

Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine.

Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MA.

Cell Host Microbe. 2014 Oct 8;16(4):495-503. doi: 10.1016/j.chom.2014.09.001. Epub 2014 Sep 25.

34.

E pluribus unum, no more: from one crystal, many conformations.

Woldeyes RA, Sivak DA, Fraser JS.

Curr Opin Struct Biol. 2014 Oct;28:56-62. doi: 10.1016/j.sbi.2014.07.005. Epub 2014 Aug 9. Review.

35.

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery.

Fischer M, Coleman RG, Fraser JS, Shoichet BK.

Nat Chem. 2014 Jul;6(7):575-83. doi: 10.1038/nchem.1954. Epub 2014 May 25.

36.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS.

Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29.

37.

Diffuse X-ray scattering to model protein motions.

Wall ME, Adams PD, Fraser JS, Sauter NK.

Structure. 2014 Feb 4;22(2):182-4. doi: 10.1016/j.str.2014.01.002.

38.

Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR.

Fenwick RB, van den Bedem H, Fraser JS, Wright PE.

Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):E445-54. doi: 10.1073/pnas.1323440111. Epub 2014 Jan 13.

39.

Protein structural ensembles are revealed by redefining X-ray electron density noise.

Lang PT, Holton JM, Fraser JS, Alber T.

Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):237-42. doi: 10.1073/pnas.1302823110. Epub 2013 Dec 20.

40.

From structure to systems: high-resolution, quantitative genetic analysis of RNA polymerase II.

Braberg H, Jin H, Moehle EA, Chan YA, Wang S, Shales M, Benschop JJ, Morris JH, Qiu C, Hu F, Tang LK, Fraser JS, Holstege FC, Hieter P, Guthrie C, Kaplan CD, Krogan NJ.

Cell. 2013 Aug 15;154(4):775-88. doi: 10.1016/j.cell.2013.07.033. Epub 2013 Aug 8.

41.

Automated identification of functional dynamic contact networks from X-ray crystallography.

van den Bedem H, Bhabha G, Yang K, Wright PE, Fraser JS.

Nat Methods. 2013 Sep;10(9):896-902. doi: 10.1038/nmeth.2592. Epub 2013 Aug 4.

42.

Thematic and spatial resolutions affect model-based predictions of tree species distribution.

Liang Y, He HS, Fraser JS, Wu Z.

PLoS One. 2013 Jul 4;8(7):e67889. doi: 10.1371/journal.pone.0067889. Print 2013.

43.

Modeling the Effects of Harvest Alternatives on Mitigating Oak Decline in a Central Hardwood Forest Landscape.

Wang WJ, He HS, Spetich MA, Shifley SR, Thompson Iii FR, Fraser JS.

PLoS One. 2013 Jun 18;8(6):e66713. doi: 10.1371/journal.pone.0066713. Print 2013.

44.

Flexible backbone sampling methods to model and design protein alternative conformations.

Ollikainen N, Smith CA, Fraser JS, Kortemme T.

Methods Enzymol. 2013;523:61-85. doi: 10.1016/B978-0-12-394292-0.00004-7.

45.

From systems to structure: bridging networks and mechanism.

Fraser JS, Gross JD, Krogan NJ.

Mol Cell. 2013 Jan 24;49(2):222-31. doi: 10.1016/j.molcel.2013.01.003. Review.

46.

CheShift-2 resolves a local inconsistency between two X-ray crystal structures.

Vila JA, Sue SC, Fraser JS, Scheraga HA, Dyson HJ.

J Biomol NMR. 2012 Oct;54(2):193-8. Epub 2012 Sep 4.

47.

Systematic functional prioritization of protein posttranslational modifications.

Beltrao P, Albanèse V, Kenner LR, Swaney DL, Burlingame A, Villén J, Lim WA, Fraser JS, Frydman J, Krogan NJ.

Cell. 2012 Jul 20;150(2):413-25. doi: 10.1016/j.cell.2012.05.036.

48.

Integrative Families and Systems Treatment: a middle path toward integrating common and specific factors in evidence-based family therapy.

Fraser JS, Solovey AD, Grove D, Lee MY, Greene GJ.

J Marital Fam Ther. 2012 Jul;38(3):515-28. doi: 10.1111/j.1752-0606.2011.00228.x. Epub 2011 Apr 19. Review.

PMID:
22804469
49.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair.

Kapp GT, Liu S, Stein A, Wong DT, Reményi A, Yeh BJ, Fraser JS, Taunton J, Lim WA, Kortemme T.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5277-82. doi: 10.1073/pnas.1114487109. Epub 2012 Mar 7.

50.

Accessing protein conformational ensembles using room-temperature X-ray crystallography.

Fraser JS, van den Bedem H, Samelson AJ, Lang PT, Holton JM, Echols N, Alber T.

Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16247-52. doi: 10.1073/pnas.1111325108. Epub 2011 Sep 14.

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