Brian Kuhlman - Publications


136 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
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/  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/  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/  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/  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/  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
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