| Year |
Citation |
Score |
| 2020 |
Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, Kuhlman B. Perturbing the energy landscape for improved packing during computational protein design. Proteins. PMID 33249652 DOI: 10.1002/prot.26030 |
1 |
|
| 2020 |
Lerner AM, Hepperla AJ, Keele GR, Meriesh HA, Yumerefendi H, Restrepo D, Zimmerman S, Bear JE, Kuhlman B, Davis IJ, Strahl BD. An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation. Genome Research. PMID 33020206 DOI: 10.1101/gr.264283.120 |
1 |
|
| 2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Kuhlman B, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/s41592-020-0848-2 |
1 |
|
| 2020 |
Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Kuhlman B, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/journal.pcbi.1007507 |
1 |
|
| 2020 |
Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, ... ... Kuhlman B, et al. Computer-based Engineering of Thermostabilized Antibody Fragments. Aiche Journal. American Institute of Chemical Engineers. 66. PMID 32336757 DOI: 10.1002/aic.16864 |
0.84 |
|
| 2019 |
Kuhlman B, Bradley P. Advances in protein structure prediction and design. Nature Reviews. Molecular Cell Biology. PMID 31417196 DOI: 10.1038/s41580-019-0163-x |
0.92 |
|
| 2018 |
Studer S, Hansen DA, Pianowski ZL, Mittl PRE, Debon A, Guffy SL, Der BS, Kuhlman B, Hilvert D. Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science (New York, N.Y.). 362: 1285-1288. PMID 30545884 DOI: 10.1126/science.aau3744 |
0.32 |
|
| 2018 |
Lerner A, Yumerefendi H, Goudy O, Strahl BD, Kuhlman B. Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution. Acs Synthetic Biology. PMID 30441907 DOI: 10.1021/acssynbio.8b00368 |
0.44 |
|
| 2018 |
DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE. A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Molecular Cell. PMID 30392931 DOI: 10.1016/j.molcel.2018.09.029 |
0.64 |
|
| 2018 |
Maguire JB, Boyken SE, Baker D, Kuhlman B. Correction to Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. Journal of Chemical Theory and Computation. PMID 30221938 DOI: 10.1021/acs.jctc.8b00883 |
1 |
|
| 2018 |
Maguire JB, Boyken SE, Baker D, Kuhlman B. Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. Journal of Chemical Theory and Computation. PMID 29652499 DOI: 10.1021/acs.jctc.8b00033 |
1 |
|
| 2018 |
Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB. Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance. Nucleic Acids Research. PMID 29506131 DOI: 10.1093/nar/gky151 |
0.64 |
|
| 2018 |
Yumerefendi H, Wang H, Dickinson DJ, Lerner A, Malkus P, Goldstein B, Hahn K, Kuhlman B. Light-dependent cytoplasmic recruitment enhances the dynamic range of a nuclear import photoswitch. Chembiochem : a European Journal of Chemical Biology. PMID 29446199 DOI: 10.1002/cbic.201700681 |
0.44 |
|
| 2018 |
Hayne CK, Yumerefendi H, Cao L, Gauer JW, Lafferty MJ, Kuhlman B, Erie DA, Neher SB. We FRET so You Don't Have To: New Models of the Lipoprotein Lipase Dimer. Biochemistry. PMID 29303250 DOI: 10.1021/acs.biochem.7b01009 |
0.44 |
|
| 2017 |
Froning KJ, Leaver-Fay A, Wu X, Phan S, Gao L, Huang F, Pustilnik A, Bacica M, Houlihan K, Chai Q, Fitchett JR, Hendle J, Kuhlman B, Demarest SJ. Computational Design of a Specific Heavy Chain/κ Light Chain Interface for Expressing Fully IgG Bispecific Antibodies. Protein Science : a Publication of the Protein Society. PMID 28726352 DOI: 10.1002/pro.3240 |
0.84 |
|
| 2017 |
Grove TL, Himes PM, Hwang S, Yumerefendi H, Bonanno JB, Kuhlman B, Almo SC, Bowers AA. Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides. Journal of the American Chemical Society. PMID 28704043 DOI: 10.1021/jacs.7b01283 |
0.44 |
|
| 2017 |
Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, ... ... Kuhlman B, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/acs.jctc.7b00125 |
1 |
|
| 2016 |
Harrison JS, Cornett EM, Goldfarb D, DaRosa PA, Li ZM, Yan F, Dickson BM, Guo AH, Cantu DV, Kaustov L, Brown PJ, Arrowsmith CH, Erie DA, Major MB, Klevit RE, ... ... Kuhlman B, et al. Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1. Elife. 5. PMID 27595565 DOI: 10.7554/eLife.17101 |
0.64 |
|
| 2016 |
Zimmerman SP, Hallett R, Bourke AM, Bear JE, Kennedy MJ, Kuhlman B. Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. Biochemistry. PMID 27529180 DOI: 10.1021/acs.biochem.6b00529 |
1 |
|
| 2016 |
Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM. LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nature Methods. PMID 27427858 DOI: 10.1038/nmeth.3926 |
0.44 |
|
| 2016 |
Guffy SL, Der BS, Kuhlman B. Probing the minimal determinants of zinc binding with computational protein design. Protein Engineering, Design & Selection : Peds. PMID 27358168 DOI: 10.1093/protein/gzw026 |
0.32 |
|
| 2016 |
Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, ... ... Kuhlman B, et al. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell. 165: 1440-1453. PMID 27259151 DOI: 10.1016/j.cell.2016.05.037 |
1 |
|
| 2016 |
King SJ, Asokan SB, Haynes EM, Zimmerman SP, Rotty JD, Alb JG, Tagliatela A, Blake DR, Lebedeva IP, Marston D, Johnson HE, Parsons M, Sharpless NE, Kuhlman B, Haugh JM, et al. Lamellipodia are critical for haptotactic sensing and response. Journal of Cell Science. PMID 27173494 DOI: 10.1242/jcs.184507 |
1 |
|
| 2016 |
Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B. Design of structurally distinct proteins using strategies inspired by evolution. Science (New York, N.Y.). 352: 687-90. PMID 27151863 DOI: 10.1126/science.aad8036 |
1 |
|
| 2016 |
Yumerefendi H, Lerner AM, Zimmerman SP, Hahn K, Bear JE, Strahl BD, Kuhlman B. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. Nature Chemical Biology. PMID 27089030 DOI: 10.1038/nchembio.2068 |
1 |
|
| 2016 |
Hill S, Harrison JS, Lewis SM, Kuhlman B, Kleiger G. Mechanism of Lysine 48 selectivity during poly-ubiquitin chain formation by the Ube2R1/2 ubiquitin-conjugating enzyme. Molecular and Cellular Biology. PMID 27044868 DOI: 10.1128/MCB.00097-16 |
0.64 |
|
| 2016 |
Leaver-Fay A, Froning KJ, Atwell S, Aldaz H, Pustilnik A, Lu F, Huang F, Yuan R, Hassanali S, Chamberlain AK, Fitchett JR, Demarest SJ, Kuhlman B. Computationally Designed Bispecific Antibodies using Negative State Repertoires. Structure (London, England : 1993). PMID 26996964 DOI: 10.1016/j.str.2016.02.013 |
1 |
|
| 2016 |
Nguyen TV, Lee JE, Sweredoski MJ, Yang SJ, Jeon SJ, Harrison JS, Yim JH, Lee SG, Handa H, Kuhlman B, Jeong JS, Reitsma JM, Park CS, Hess S, Deshaies RJ. Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon. Molecular Cell. 61: 809-820. PMID 26990986 DOI: 10.1016/j.molcel.2016.02.032 |
1 |
|
| 2016 |
Zimmerman SP, Kuhlman B, Yumerefendi H. Engineering and Application of LOV2-Based Photoswitches Methods in Enzymology. 580: 169-190. DOI: 10.1016/bs.mie.2016.05.058 |
1 |
|
| 2015 |
Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B. Data in support of UbSRD: The Ubiquitin Structural Relational Database. Data in Brief. 5: 605-15. PMID 26958617 DOI: 10.1016/j.dib.2015.10.007 |
0.64 |
|
| 2015 |
Kim DN, Jacobs TM, Kuhlman B. Boosting protein stability with the computational design of β-sheet surfaces. Protein Science : a Publication of the Protein Society. PMID 26701383 DOI: 10.1002/pro.2869 |
1 |
|
| 2015 |
Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B. Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. Protein Engineering, Design & Selection : Peds. PMID 26489878 DOI: 10.1093/protein/gzv055 |
1 |
|
| 2015 |
Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B. Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide. Acs Synthetic Biology. PMID 26474029 DOI: 10.1021/acssynbio.5b00119 |
1 |
|
| 2015 |
Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B. UbSRD: The Ubiquitin Structural Relational Database. Journal of Molecular Biology. PMID 26392143 DOI: 10.1016/j.jmb.2015.09.011 |
1 |
|
| 2015 |
Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H. Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature. 525: 333-8. PMID 26352471 DOI: 10.1038/nature15257 |
1 |
|
| 2015 |
Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, Gonzalez-Rivera K, Williams T, Li L, Weinreb V, Collier M, Chandrasekaran SN, Ambroggio X, Kuhlman B, Carter CW. Functional Class I and II Amino Acid Activating Enzymes Can Be Coded by Opposite Strands of the Same Gene. The Journal of Biological Chemistry. PMID 26088142 DOI: 10.1074/jbc.M115.642876 |
1 |
|
| 2015 |
Yumerefendi H, Dickinson DJ, Wang H, Zimmerman SP, Bear JE, Goldstein B, Hahn K, Kuhlman B. Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation. Plos One. 10: e0128443. PMID 26083500 DOI: 10.1371/journal.pone.0128443 |
1 |
|
| 2015 |
O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/ct500864r |
1 |
|
| 2015 |
Wu X, Sereno AJ, Huang F, Lewis SM, Lieu RL, Weldon C, Torres C, Fine C, Batt MA, Fitchett JR, Glasebrook AL, Kuhlman B, Demarest SJ. Fab-based bispecific antibody formats with robust biophysical properties and biological activity. Mabs. 7: 470-82. PMID 25774965 DOI: 10.1080/19420862.2015.1022694 |
1 |
|
| 2015 |
Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic Acids Research. 43: e34. PMID 25539925 DOI: 10.1093/nar/gku1323 |
1 |
|
| 2015 |
Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proceedings of the National Academy of Sciences of the United States of America. 112: 112-7. PMID 25535392 DOI: 10.1073/pnas.1417910112 |
1 |
|
| 2015 |
Sandoval D, Hill S, Ziemba A, Lewis S, Kuhlman B, Kleiger G. Ubiquitin-conjugating enzyme Cdc34 and ubiquitin ligase Skp1-cullin-F-box ligase (SCF) interact through multiple conformations. The Journal of Biological Chemistry. 290: 1106-18. PMID 25425648 DOI: 10.1074/jbc.M114.615559 |
1 |
|
| 2015 |
Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B. Computational de novo design of a four-helix bundle protein--DND_4HB. Protein Science : a Publication of the Protein Society. 24: 434-45. PMID 25287625 DOI: 10.1002/pro.2577 |
0.32 |
|
| 2015 |
Harrison JS, Jacobs TM, Houlihan K, Van Doorslaer K, Kuhlman B. Data in support of UbSRD: The Ubiquitin Structural Relational Database Data in Brief. 5: 605-615. DOI: 10.1016/j.dib.2015.10.007 |
1 |
|
| 2014 |
Strande NT, Carvajal-Garcia J, Hallett RA, Waters CA, Roberts SA, Strom C, Kuhlman B, Ramsden DA. Requirements for 5'dRP/AP lyase activity in Ku. Nucleic Acids Research. 42: 11136-43. PMID 25200085 DOI: 10.1093/nar/gku796 |
1 |
|
| 2014 |
Carter CW, Li L, Weinreb V, Collier M, Gonzalez-Rivera K, Jimenez-Rodriguez M, Erdogan O, Kuhlman B, Ambroggio X, Williams T, Chandrasekharan SN. The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed. Biology Direct. 9: 11. PMID 24927791 DOI: 10.1186/1745-6150-9-11 |
1 |
|
| 2014 |
Lewis SM, Wu X, Pustilnik A, Sereno A, Huang F, Rick HL, Guntas G, Leaver-Fay A, Smith EM, Ho C, Hansen-Estruch C, Chamberlain AK, Truhlar SM, Conner EM, Atwell S, ... Kuhlman B, et al. Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Nature Biotechnology. 32: 191-8. PMID 24463572 DOI: 10.1038/nbt.2797 |
1 |
|
| 2013 |
Jacobs TM, Kuhlman B. Using anchoring motifs for the computational design of protein-protein interactions. Biochemical Society Transactions. 41: 1141-5. PMID 24059499 DOI: 10.1042/BST20130108 |
1 |
|
| 2013 |
Der BS, Kuhlman B. Cages from coils. Nature Biotechnology. 31: 809-10. PMID 24022157 DOI: 10.1038/nbt.2670 |
1 |
|
| 2013 |
Kamadurai HB, Qiu Y, Deng A, Harrison JS, Macdonald C, Actis M, Rodrigues P, Miller DJ, Souphron J, Lewis SM, Kurinov I, Fujii N, Hammel M, Piper R, Kuhlman B, et al. Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Elife. 2: e00828. PMID 23936628 DOI: 10.7554/eLife.00828 |
1 |
|
| 2013 |
Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/journal.pone.0067051 |
1 |
|
| 2013 |
Harrison JS, Higgins CD, O'Meara MJ, Koellhoffer JF, Kuhlman BA, Lai JR. Role of electrostatic repulsion in controlling pH-dependent conformational changes of viral fusion proteins. Structure (London, England : 1993). 21: 1085-96. PMID 23823327 DOI: 10.1016/j.str.2013.05.009 |
1 |
|
| 2013 |
Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. Plos One. 8: e64363. PMID 23741319 DOI: 10.1371/journal.pone.0064363 |
1 |
|
| 2013 |
Der BS, Kuhlman B. Strategies to control the binding mode of de novo designed protein interactions. Current Opinion in Structural Biology. 23: 639-46. PMID 23731800 DOI: 10.1016/j.sbi.2013.04.010 |
1 |
|
| 2013 |
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/journal.pone.0063906 |
1 |
|
| 2013 |
Der BS, Jha RK, Jha RK, Lewis SM, Thompson PM, Guntas G, Kuhlman B. Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding. Proteins. 81: 1245-55. PMID 23504819 DOI: 10.1002/PROT.24379 |
1 |
|
| 2013 |
Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, ... ... Kuhlman B, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0 |
1 |
|
| 2013 |
Zhang J, Lewis SM, Kuhlman B, Lee AL. Supertertiary structure of the MAGUK core from PSD-95. Structure (London, England : 1993). 21: 402-13. PMID 23395180 DOI: 10.1016/j.str.2012.12.014 |
1 |
|
| 2013 |
Choi EJ, Jacak R, Kuhlman B. A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins. Protein Engineering, Design & Selection : Peds. 26: 283-9. PMID 23341643 DOI: 10.1093/protein/gzs108 |
1 |
|
| 2013 |
Baker R, Lewis SM, Sasaki AT, Wilkerson EM, Locasale JW, Cantley LC, Kuhlman B, Dohlman HG, Campbell SL. Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function. Nature Structural & Molecular Biology. 20: 46-52. PMID 23178454 DOI: 10.1038/nsmb.2430 |
1 |
|
| 2013 |
Stranges PB, Kuhlman B. A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Science : a Publication of the Protein Society. 22: 74-82. PMID 23139141 DOI: 10.1002/pro.2187 |
1 |
|
| 2012 |
Murphy GS, Mills JL, Miley MJ, Machius M, Szyperski T, Kuhlman B. Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core. Structure (London, England : 1993). 20: 1086-96. PMID 22632833 DOI: 10.1016/j.str.2012.03.026 |
1 |
|
| 2012 |
Lungu OI, Hallett RA, Choi EJ, Aiken MJ, Hahn KM, Kuhlman B. Designing photoswitchable peptides using the AsLOV2 domain. Chemistry & Biology. 19: 507-17. PMID 22520757 DOI: 10.1016/j.chembiol.2012.07.009 |
1 |
|
| 2012 |
Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, ... ... Kuhlman B, et al. Structure-based design of supercharged, highly thermoresistant antibodies. Chemistry & Biology. 19: 449-55. PMID 22520751 DOI: 10.1016/j.chembiol.2012.01.018 |
1 |
|
| 2012 |
Der BS, Edwards DR, Kuhlman B. Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering. Biochemistry. 51: 3933-40. PMID 22510088 DOI: 10.1021/bi201881p |
1 |
|
| 2012 |
Renfrew PD, Choi EJ, Bonneau R, Kuhlman B. Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. Plos One. 7: e32637. PMID 22431978 DOI: 10.1371/journal.pone.0032637 |
1 |
|
| 2012 |
Guntas G, Kuhlman B. Redesigning the NEDD8 pathway with a bacterial genetic screen for ubiquitin-like molecule transfer. Journal of Molecular Biology. 418: 161-6. PMID 22391419 DOI: 10.1016/j.jmb.2012.02.036 |
1 |
|
| 2012 |
Jacak R, Leaver-Fay A, Kuhlman B. Computational protein design with explicit consideration of surface hydrophobic patches. Proteins. 80: 825-38. PMID 22223219 DOI: 10.1002/prot.23241 |
1 |
|
| 2012 |
Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. Journal of the American Chemical Society. 134: 375-85. PMID 22092237 DOI: 10.1021/ja208015j |
1 |
|
| 2011 |
Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B. Computational design of a symmetric homodimer using β-strand assembly. Proceedings of the National Academy of Sciences of the United States of America. 108: 20562-7. PMID 22143762 DOI: 10.1073/pnas.1115124108 |
1 |
|
| 2011 |
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Kuhlman B, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/j.jmb.2011.09.031 |
1 |
|
| 2011 |
Jha RK, Wu YI, Zawistowski JS, MacNevin C, Hahn KM, Kuhlman B. Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications. Journal of Molecular Biology. 413: 513-22. PMID 21888918 DOI: 10.1016/j.jmb.2011.08.022 |
1 |
|
| 2011 |
Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B. A generic program for multistate protein design. Plos One. 6: e20937. PMID 21754981 DOI: 10.1371/journal.pone.0020937 |
1 |
|
| 2011 |
Lewis SM, Kuhlman BA. Anchored design of protein-protein interfaces. Plos One. 6: e20872. PMID 21698112 DOI: 10.1371/journal.pone.0020872 |
1 |
|
| 2011 |
Gulyani A, Vitriol E, Allen R, Wu J, Gremyachinskiy D, Lewis S, Dewar B, Graves LM, Kay BK, Kuhlman B, Elston T, Hahn KM. A biosensor generated via high-throughput screening quantifies cell edge Src dynamics. Nature Chemical Biology. 7: 437-44. PMID 21666688 DOI: 10.1038/nchembio.585 |
1 |
|
| 2011 |
Der BS, Kuhlman B. Biochemistry. From computational design to a protein that binds. Science (New York, N.Y.). 332: 801-2. PMID 21566181 DOI: 10.1126/science.1207082 |
1 |
|
| 2011 |
Saha A, Lewis S, Kleiger G, Kuhlman B, Deshaies RJ. Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate. Molecular Cell. 42: 75-83. PMID 21474069 DOI: 10.1016/j.molcel.2011.03.016 |
1 |
|
| 2011 |
Sammond DW, Bosch DE, Butterfoss GL, Purbeck C, Machius M, Siderovski DP, Kuhlman B. Computational design of the sequence and structure of a protein-binding peptide. Journal of the American Chemical Society. 133: 4190-2. PMID 21388199 DOI: 10.1021/ja110296z |
1 |
|
| 2011 |
Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Kuhlman B, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6 |
1 |
|
| 2011 |
Bosch DE, Kimple AJ, Sammond DW, Muller RE, Miley MJ, Machius M, Kuhlman B, Willard FS, Siderovski DP. Structural determinants of affinity enhancement between GoLoco motifs and G-protein alpha subunit mutants. The Journal of Biological Chemistry. 286: 3351-8. PMID 21115486 DOI: 10.1074/jbc.M110.190496 |
1 |
|
| 2010 |
Guntas G, Purbeck C, Kuhlman B. Engineering a protein-protein interface using a computationally designed library. Proceedings of the National Academy of Sciences of the United States of America. 107: 19296-301. PMID 20974935 DOI: 10.1073/pnas.1006528107 |
1 |
|
| 2010 |
Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW. Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation. The Journal of Biological Chemistry. 285: 38590-601. PMID 20864539 DOI: 10.1074/jbc.M110.136911 |
1 |
|
| 2010 |
Hahn KM, Kuhlman B. Hold me tightly LOV. Nature Methods. 7: 595, 597. PMID 20676078 DOI: 10.1038/nmeth0810-595 |
1 |
|
| 2010 |
Jha RK, Leaver-Fay A, Yin S, Wu Y, Butterfoss GL, Szyperski T, Dokholyan NV, Kuhlman B. Computational design of a PAK1 binding protein. Journal of Molecular Biology. 400: 257-70. PMID 20460129 DOI: 10.1016/j.jmb.2010.05.006 |
1 |
|
| 2010 |
Salgado EN, Ambroggio XI, Brodin JD, Lewis RA, Kuhlman B, Tezcan FA. Metal templated design of protein interfaces. Proceedings of the National Academy of Sciences of the United States of America. 107: 1827-32. PMID 20080561 DOI: 10.1073/pnas.0906852107 |
1 |
|
| 2010 |
Purbeck C, Eletr ZM, Kuhlman B. Kinetics of the transfer of ubiquitin from UbcH7 to E6AP. Biochemistry. 49: 1361-3. PMID 20039703 DOI: 10.1021/bi9014693 |
1 |
|
| 2010 |
Sammond DW, Eletr ZM, Purbeck C, Kuhlman B. Computational design of second-site suppressor mutations at protein-protein interfaces. Proteins. 78: 1055-65. PMID 19899154 DOI: 10.1002/prot.22631 |
1 |
|
| 2009 |
Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 139: 957-68. PMID 19945379 DOI: 10.1016/j.cell.2009.10.030 |
1 |
|
| 2009 |
Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R. A preliminary survey of the peptoid folding landscape. Journal of the American Chemical Society. 131: 16798-807. PMID 19919145 DOI: 10.1021/ja905267k |
1 |
|
| 2009 |
Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM. A genetically encoded photoactivatable Rac controls the motility of living cells. Nature. 461: 104-8. PMID 19693014 DOI: 10.1038/nature08241 |
1 |
|
| 2009 |
Kuhlman B, DeGrado WF. Engineering and design: editorial overview. Current Opinion in Structural Biology. 19: 440-1. PMID 19683427 DOI: 10.1016/j.sbi.2009.07.010 |
1 |
|
| 2009 |
Karanicolas J, Kuhlman B. Computational design of affinity and specificity at protein-protein interfaces. Current Opinion in Structural Biology. 19: 458-63. PMID 19646858 DOI: 10.1016/j.sbi.2009.07.005 |
1 |
|
| 2009 |
Torres MP, Lee MJ, Ding F, Purbeck C, Kuhlman B, Dokholyan NV, Dohlman HG. G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. The Journal of Biological Chemistry. 284: 8940-50. PMID 19176477 DOI: 10.1074/jbc.M809058200 |
1 |
|
| 2008 |
Hu X, Wang H, Ke H, Kuhlman B. Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design. Structure (London, England : 1993). 16: 1799-805. PMID 19081056 DOI: 10.1016/j.str.2008.09.013 |
1 |
|
| 2008 |
Renfrew PD, Butterfoss GL, Kuhlman B. Using quantum mechanics to improve estimates of amino acid side chain rotamer energies. Proteins. 71: 1637-46. PMID 18076032 DOI: 10.1002/prot.21845 |
1 |
|
| 2008 |
Leaver-Fay A, Snoeyink J, Kuhlman B. On-the-fly rotamer pair energy evaluation in protein design Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4983: 343-354. DOI: 10.1007/978-3-540-79450-9_32 |
1 |
|
| 2007 |
Hu X, Wang H, Ke H, Kuhlman B. High-resolution design of a protein loop. Proceedings of the National Academy of Sciences of the United States of America. 104: 17668-73. PMID 17971437 DOI: 10.1073/pnas.0707977104 |
1 |
|
| 2007 |
Kapustina M, Weinreb V, Li L, Kuhlman B, Carter CW. A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase. Structure (London, England : 1993). 15: 1272-84. PMID 17937916 DOI: 10.1016/j.str.2007.08.010 |
1 |
|
| 2007 |
Sammond DW, Eletr ZM, Purbeck C, Kimple RJ, Siderovski DP, Kuhlman B. Structure-based protocol for identifying mutations that enhance protein-protein binding affinities. Journal of Molecular Biology. 371: 1392-404. PMID 17603074 DOI: 10.1016/j.jmb.2007.05.096 |
1 |
|
| 2007 |
Eletr ZM, Kuhlman B. Sequence determinants of E2-E6AP binding affinity and specificity. Journal of Molecular Biology. 369: 419-28. PMID 17433363 DOI: 10.1016/j.jmb.2007.03.026 |
1 |
|
| 2007 |
Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL, Kuhlman B, Carter CW. A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Molecular Cell. 25: 851-62. PMID 17386262 DOI: 10.1016/j.molcel.2007.02.010 |
1 |
|
| 2007 |
Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. Maintaining solvent accessible surface area under rotamer substitution for protein design. Journal of Computational Chemistry. 28: 1336-41. PMID 17285560 DOI: 10.1002/jcc.20626 |
1 |
|
| 2007 |
Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. Journal of Molecular Biology. 366: 1209-21. PMID 17196978 DOI: 10.1016/j.jmb.2006.11.080 |
1 |
|
| 2006 |
Johnston CA, Lobanova ES, Shavkunov AS, Low J, Ramer JK, Blaesius R, Fredericks Z, Willard FS, Kuhlman B, Arshavsky VY, Siderovski DP. Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer. Biochemistry. 45: 11390-400. PMID 16981699 DOI: 10.1021/bi0613832 |
1 |
|
| 2006 |
Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/j.jmb.2006.07.092 |
1 |
|
| 2006 |
Junghans U, Polle A, Düchting P, Weiler E, Kuhlman B, Gruber F, Teichmann T. Adaptation to high salinity in poplar involves changes in xylem anatomy and auxin physiology. Plant, Cell & Environment. 29: 1519-31. PMID 16898015 DOI: 10.1111/j.1365-3040.2006.01529.x |
1 |
|
| 2006 |
Liu Y, Kuhlman B. RosettaDesign server for protein design. Nucleic Acids Research. 34: W235-8. PMID 16845000 DOI: 10.1093/nar/gkl163 |
1 |
|
| 2006 |
Ambroggio XI, Kuhlman B. Design of protein conformational switches. Current Opinion in Structural Biology. 16: 525-30. PMID 16765587 DOI: 10.1016/j.sbi.2006.05.014 |
1 |
|
| 2006 |
Butterfoss GL, Kuhlman B. Computer-based design of novel protein structures. Annual Review of Biophysics and Biomolecular Structure. 35: 49-65. PMID 16689627 DOI: 10.1146/annurev.biophys.35.040405.102046 |
1 |
|
| 2006 |
Ambroggio XI, Kuhlman B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. Journal of the American Chemical Society. 128: 1154-61. PMID 16433531 DOI: 10.1021/ja054718w |
1 |
|
| 2006 |
Hu X, Kuhlman B. Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins. 62: 739-48. PMID 16317667 DOI: 10.1002/prot.20786 |
1 |
|
| 2005 |
Eletr ZM, Huang DT, Duda DM, Schulman BA, Kuhlman B. E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nature Structural & Molecular Biology. 12: 933-4. PMID 16142244 DOI: 10.1038/nsmb984 |
1 |
|
| 2005 |
Leaver-Fay A, Kuhlman B, Snoeyink J. An adaptive dynamic programming algorithm for the side chain placement problem. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 16-27. PMID 15759610 |
1 |
|
| 2005 |
Jiang L, Kuhlman B, Kortemme T, Baker D. A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58: 893-904. PMID 15651050 DOI: 10.1002/prot.20347 |
1 |
|
| 2005 |
Leaver-Fay A, Kuhlman B, Snoeyink J. Rotamer-pair energy calculations using a trie data structure Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692: 389-400. DOI: 10.1007/11557067_32 |
1 |
|
| 2004 |
von Grotthuss M, Wyrwicz LS, Pas J, Rychlewski L. Predicting protein structures accurately. Science (New York, N.Y.). 304: 1597-9; author reply. PMID 15192202 DOI: 10.1126/science.304.5677.1597b |
1 |
|
| 2004 |
Kuhlman B, Baker D. Exploring folding free energy landscapes using computational protein design. Current Opinion in Structural Biology. 14: 89-95. PMID 15102454 DOI: 10.1016/j.sbi.2004.01.002 |
1 |
|
| 2003 |
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science (New York, N.Y.). 302: 1364-8. PMID 14631033 DOI: 10.1126/science.1089427 |
1 |
|
| 2003 |
Dantas G, Kuhlman B, Callender D, Wong M, Baker D. A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of Molecular Biology. 332: 449-60. PMID 12948494 DOI: 10.1016/S0022-2836(03)00888-X |
1 |
|
| 2003 |
Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53: 76-87. PMID 12945051 DOI: 10.1002/prot.10454 |
1 |
|
| 2003 |
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology. 331: 281-99. PMID 12875852 DOI: 10.1016/S0022-2836(03)00670-3 |
1 |
|
| 2002 |
Nauli S, Kuhlman B, Le Trong I, Stenkamp RE, Teller D, Baker D. Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Science : a Publication of the Protein Society. 11: 2924-31. PMID 12441390 DOI: 10.1110/ps.0216902 |
1 |
|
| 2002 |
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of Molecular Biology. 315: 471-7. PMID 11786026 DOI: 10.1006/jmbi.2001.5229 |
1 |
|
| 2001 |
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98: 10687-91. PMID 11526208 DOI: 10.1073/pnas.181354398 |
1 |
|
| 2001 |
Nauli S, Kuhlman B, Baker D. Computer-based redesign of a protein folding pathway. Nature Structural Biology. 8: 602-5. PMID 11427890 DOI: 10.1038/89638 |
1 |
|
| 2000 |
Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97: 10383-8. PMID 10984534 |
1 |
|
| 1999 |
Luisi DL, Kuhlman B, Sideras K, Evans PA, Raleigh DP. Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed alpha/beta protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L9. Journal of Molecular Biology. 289: 167-74. PMID 10339414 DOI: 10.1006/jmbi.1999.2742 |
1 |
|
| 1999 |
Sato S, Kuhlman B, Wu WJ, Raleigh DP. Folding of the multidomain ribosomal protein L9: the two domains fold independently with remarkably different rates. Biochemistry. 38: 5643-50. PMID 10220353 DOI: 10.1021/bi9830314 |
1 |
|
| 1999 |
Kuhlman B, Luisi DL, Young P, Raleigh DP. pKa values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions. Biochemistry. 38: 4896-903. PMID 10200179 DOI: 10.1021/bi982931h |
1 |
|
| 1998 |
Kuhlman B, Luisi DL, Evans PA, Raleigh DP. Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9. Journal of Molecular Biology. 284: 1661-70. PMID 9878377 DOI: 10.1006/jmbi.1998.2246 |
1 |
|
| 1998 |
Kuhlman B, Raleigh DP. Global analysis of the thermal and chemical denaturation of the N-terminal domain of the ribosomal protein L9 in H2O and D2O. Determination of the thermodynamic parameters, deltaH(o), deltaS(o), and deltaC(o)p and evaluation of solvent isotope effects. Protein Science : a Publication of the Protein Society. 7: 2405-12. PMID 9828007 DOI: 10.1002/pro.5560071118 |
1 |
|
| 1998 |
Vugmeyster L, Kuhlman B, Raleigh DP. Amide proton exchange measurements as a probe of the stability and dynamics of the N-terminal domain of the ribosomal protein L9: comparison with the intact protein. Protein Science : a Publication of the Protein Society. 7: 1994-7. PMID 9761480 DOI: 10.1002/pro.5560070915 |
1 |
|
| 1998 |
Spector S, Kuhlman B, Fairman R, Wong E, Boice JA, Raleigh DP. Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex. Journal of Molecular Biology. 276: 479-89. PMID 9512717 DOI: 10.1006/jmbi.1997.1522 |
1 |
|
| 1998 |
Kuhlman B, Boice JA, Fairman R, Raleigh DP. Structure and stability of the N-terminal domain of the ribosomal protein L9: evidence for rapid two-state folding. Biochemistry. 37: 1025-32. PMID 9454593 DOI: 10.1021/bi972352x |
1 |
|
| 1997 |
Kuhlman B, Yang HY, Boice JA, Fairman R, Raleigh DP. An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability. Journal of Molecular Biology. 270: 640-7. PMID 9245593 DOI: 10.1006/jmbi.1997.1146 |
1 |
|
| 1997 |
Kuhlman B, Boice JA, Wu WJ, Fairman R, Raleigh DP. Calcium binding peptides from alpha-lactalbumin: implications for protein folding and stability. Biochemistry. 36: 4607-15. PMID 9109670 DOI: 10.1021/bi962901j |
1 |
|
| Show low-probability matches. |