Publications

2023

Cummins MC, Tripathy A, Sondek J, Kuhlman B, (2023) De novo design of stable proteins that efficaciously inhibit oncogenic G proteins. Protein Sci 32:e4713. PMCID: PMCID:PMC10360382

Phan TTN, Hvasta MG, Kudlacek ST, Thiono DJ, Tripathy A, Nicely NI, Silva AM de, Kuhlman B, (2022) A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines. J Biol Chem 298:102079. PMCID: PMCID:PMC9249817

Goudy OJ, Peng A, Tripathy A, Kuhlman B, (2023) Design of a protease‐activated PD‐L1 inhibitor. Protein Sci 32:e4578. PMCID: PMCID:PMC9926466

Park R, Ongpipattanakul C, Nair SK, Bowers AA, Kuhlman B, (2023) Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nat Chem Biol 19:460–467. PMCID: PMCID:PMC10065947

Goudy OJ, Nallathambi A, Kinjo T, Randolph N, Kuhlman B, (2023) In silico evolution of protein binders with deep learning models for structure prediction and sequence design. bioRxiv doi:10.1101/2023.05.03.539278. PMCID: PMCID:PMC10187191

Guffy SL, Pulavarti SVSRK, Harrison J, Fleming D, Szyperski T, Kuhlman B, (2023) Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry-us 62:770–781. PMCID: PMCID:PMC9939277

Randolph N, Kuhlman B, (2023) Invariant point message passing for protein side chain packing and design. doi:10.1101/2023.08.03.551328.

Dieckhaus H, Brocidiacono M, Randolph N, Kuhlman B, (2023) Transfer learning to leverage larger datasets for improved prediction of protein stability changes. bioRxiv doi:10.1101/2023.07.27.550881. PMCID: PMCID:PMC10402116

 

2022

Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B, (2022) AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein Sci 31:e4368. PMCID: PMCID:PMC9207892

Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML, (2022) Comparative Analysis of Sulfonium−π, Ammonium−π, and Sulfur−π Interactions and Relevance to SAM-Dependent Methyltransferases. J Am Chem Soc 144:2535–2545.

Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T, (2022) From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 126:1212–1231.

Thieker DF, Maguire JB, Kudlacek ST, Leaver-Fay A, Lyskov S, Kuhlman B, (2022) Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein Sci Publ Protein Soc 31:e4428. PMCID: PMCID:PMC9490798

 

2021

Martinez NG, Thieker DF, Carey LM, Rasquinha JA, Kistler SK, Kuhlman BA, Campbell SL, (2021) Biophysical and Structural Characterization of Novel RAS-Binding Domains (RBDs) of PI3Kα and PI3Kγ. J Mol Biol 433:166838.

Kudlacek ST, Metz S, Thiono D, Payne AM, Phan TTN, Tian S, Forsberg LJ, Maguire J, Seim I, Zhang S, Tripathy A, Harrison J, Nicely NI, Soman S, McCracken MK, Gromowski GD, Jarman RG, Premkumar L, Silva AM de, Kuhlman B, (2021) Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Sci Adv 7:eabg4084. PMCID: PMCID:PMC8519570

Hussain M, Cummins MC, Endo-Streeter S, Sondek J, Kuhlman B, (2021) Designer proteins that competitively inhibit Gαq by targeting its effector site. J Biol Chem 297:101348. PMCID: PMCID:PMC8633581

Leman JK, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, Conchúir SÓ, Burman SSR, Samanta R, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R, (2021) Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 12:6947. PMCID: PMCID:PMC8630030

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, (2021) Perturbing the energy landscape for improved packing during computational protein design. Proteins Struct Funct Bioinform 89:436–449. PMCID: PMCID:PMC8299543

Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte JW, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner BD, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL, Schief W, Kuhlman B, Siegel JB, Gray JJ, (2021) PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist 2:108–122.

 

2020

Teets FD, Watanabe T, Hahn KM, Kuhlman B, (2020) A Computational Protocol for Regulating Protein Binding Reactions with a Light-Sensitive Protein Dimer. J Mol Biol 432:805–814.

Lerner AM, Hepperla AJ, Keele GR, Meriesh HA, Yumerefendi H, Restrepo D, Zimmerman S, Bear JE, Kuhlman B, Davis IJ, Strahl BD, (2020) An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation. Genome Res 30:1605–1617. PMCID: PMCID:PMC7605256

Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Consortium R, Bystroff C, Schief W, Gront D, Schueler-Furman O, Baker D, Bradley P, Dunbrack R, Kortemme T, Leaver-Fay A, Strauss CEM, Meiler J, Kuhlman B, Gray JJ, Bonneau R, (2020) Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Comput Biol 16:e1007507. PMCID: PMCID:PMC7197760

Froning K, Maguire J, Sereno A, Huang F, Chang S, Weichert K, Frommelt AJ, Dong J, Wu X, Austin H, Conner EM, Fitchett JR, Heng AR, Balasubramaniam D, Hilgers MT, Kuhlman B, Demarest SJ, (2020) Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics. Nat Commun 11:2330. PMCID: PMCID:PMC7214467

Thomas A, Thiono DJ, Kudlacek ST, Forsberg J, Premkumar L, Tian S, Kuhlman B, Silva AM de, Metz SW, (2020) Dimerization of Dengue Virus E Subunits Impacts Antibody Function and Domain Focus. J Virol 94. PMCID: PMCID:PMC7459570

Landoni E, Fucá G, Wang J, Chirasani VR, Yao Z, Dukhovlinova E, Ferrone S, Savoldo B, Hong LK, Shou P, Musio S, Padelli F, Finocchiaro G, Droste M, Kuhlman B, Shamshiev A, Pellegatta S, Dokholyan NV, Dotti G, (2020) Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling. Cancer Immunol Res 9:441–453. PMCID: PMCID:PMC8137530

 

2019

Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee C, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD, (2019) Computer‐based engineering of thermostabilized antibody fragments. Aiche J 66. PMCID: PMCID:PMC7181397

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, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, Jong RMD, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Bonneau R, et al., (2019) Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 17:665–680. PMCID: PMCID:PMC7603796

Stone OJ, Pankow N, Liu B, Sharma VP, Eddy RJ, Wang H, Putz AT, Teets FD, Kuhlman B, Condeelis JS, Hahn KM, (2019) Optogenetic control of cofilin and αTAT in living cells using Z-lock. Nat Chem Biol 15:1183–1190. PMCID: PMCID:PMC6873228

 

2018

DaRosa PA, Harrison JS, Zelter A, Davis TN, Brzovic P, Kuhlman B, Klevit RE, (2018) A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation. Molecular cell 72:753-765.e6.

Hussain M, Angus SP, Kuhlman B, (2018) Engineering a Protein Binder Specific for p38α with Interface Expansion. Biochemistry 57:4526–4535.

Lerner AM, Yumerefendi H, Goudy OJ, Strahl BD, Kuhlman B, (2018) Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution. ACS synthetic biology 7:2898–2907.

Studer S, Hansen DA, Pianowski ZL, Mittl PRE, Debon A, Guffy SL, Der BS, Kuhlman B, Hilvert D, (2018) Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science 362:1285–1288.

Yumerefendi H, Wang H, Dickinson DJ, Lerner AM, Malkus P, Goldstein B, Hahn K, Kuhlman B, (2018) Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. Chembiochem : a European journal of chemical biology 42:443.

Guffy SL, Teets FD, Langlois MI, Kuhlman B, (2018) Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program. J Chem Inf Model 58:895–901. PMCID: PMCID:PMC5975180

Maguire JB, Boyken SE, Baker D, Kuhlman B, (2018) Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. J Chem Theory Comput 14:2751–2760. PMCID: PMCID:PMC5940506

Hayne CK, Yumerefendi H, Cao L, Gauer JW, Lafferty MJ, Kuhlman B, Erie DA, Neher SB, (2018) We FRET so You Don’t Have To: New Models of the Lipoprotein Lipase Dimer. Biochemistry 57:241–254.

 

2017

Zimmerman SP, Asokan SB, Kuhlman B, Bear JE, (2017) Cells lay their own tracks – optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration. Journal of Cell Science 130:2971–2983.

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, (2017) Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies. Protein Science 26:2021–2038.

Grove TL, Himes PM, Hwang S, Yumerefendi H, Bonanno JB, Kuhlman B, Almo SC, Bowers AA, (2017) Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides. Journal of the American Chemical Society 139:11734–11744.

 

2016

Jacobs TM, Williams B, Williams T, Xu X, Eletsky A, Federizon JF, Szyperski T, Kuhlman B, (2016) Design of structurally distinct proteins using strategies inspired by evolution. Science 352:687–690. PMCID: PMCID:PMC4934125

Kim DN, Jacobs TM, Kuhlman B, (2016) Boosting protein stability with the computational design of β-sheet surfaces. Protein Science 25:702–710.

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, (2016) Computationally Designed Bispecific Antibodies using Negative State Repertoires. Structure (London, England : 1993) 24:641–651.

Hallett RA, Zimmerman SP, Yumerefendi H, Bear JE, Kuhlman B, (2016) Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide. ACS synthetic biology 5:53–64.

Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu K-P, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters J-M, Stark H, Schulman BA, (2016) Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell 165:1440–1453.

Guntas G, Lewis SM, Mulvaney KM, Cloer EW, Tripathy A, Lane TR, Major MB, Kuhlman B, (2016) Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display. Protein engineering, design & selection : PEDS 29:1–9.

Zimmerman SP, Kuhlman B, Yumerefendi H, (2016) Engineering and Application of LOV2-Based Photoswitches. Methods in enzymology 580:169–190.

Nguyen TV, Lee JE, Sweredoski MJ, Yang S-J, Jeon S-J, Harrison JS, Yim J-H, Lee SG, Handa H, Kuhlman B, Jeong J-S, Reitsma JM, Park C-S, Hess S, Deshaies RJ, (2016) Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon. Molecular cell 61:809–820.

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, Krajewski K, Kuhlman B, Strahl BD, Rothbart SB, (2016) Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1. eLife 5:818.

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, Bear JE, (2016) Lamellipodia are crucial for haptotactic sensing and response. Journal of Cell Science 129:2329–2342.

Yumerefendi H, Lerner AM, Zimmerman SP, Hahn K, Bear JE, Strahl BD, Kuhlman B, (2016) Light-induced nuclear export reveals rapid dynamics of epigenetic modifications. Nat Chem Biol 12:399–401. PMCID: PMCID:PMC4888063

Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM, (2016) LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nature methods 13:755–758.

Hill S, Harrison JS, Lewis SM, Kuhlman B, Kleiger G, (2016) Mechanism of Lysine 48 selectivity during poly-ubiquitin chain formation by the Ube2R1/2 ubiquitin-conjugating enzyme. Molecular and Cellular Biology doi:10.1128/mcb.00097-16.

Guffy SL, Der BS, Kuhlman B, (2016) Probing the minimal determinants of zinc binding with computational protein design. Protein engineering, design & selection : PEDS 29:327–338.

Zimmerman SP, Hallett RA, Bourke AM, Bear JE, Kennedy MJ, Kuhlman B, (2016) Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization. Biochemistry 55:5264–5271.

 

2015

O’Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B, (2015) Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. J Chem Theory Comput 11:609–622. PMCID: PMCID:PMC4390092

Yumerefendi H, Dickinson DJ, Wang H, Zimmerman SP, Bear JE, Goldstein B, Hahn K, Kuhlman B, (2015) Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation. PloS one 10:e0128443.

Harrison JS, Jacobs TM, Houlihan K, Doorslaer KV, Kuhlman B, (2015) Data in support of UbSRD: The Ubiquitin Structural Relational Database. Data Brief 5:605–615. PMCID: PMCID:PMC4773368

Guntas G, Hallett RA, Zimmerman SP, Williams T, Yumerefendi H, Bear JE, Kuhlman B, (2015) Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc National Acad Sci 112:112–117. PMCID: PMCID:PMC4291625

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, (2015) Fab-based bispecific antibody formats with robust biophysical properties and biological activity. mAbs 7:470–482.

Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H, (2015) Labelling and optical erasure of synaptic memory traces in the motor cortex. Nature 525:333–338.

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, (2015) Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene*. J Biol Chem 290:19710–19725. PMCID: PMCID:PMC4528134

Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A, (2015) SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic acids research 43:e34–e34.

Sandoval D, Hill S, Ziemba A, Lewis S, Kuhlman B, Kleiger G, (2015) Ubiquitin-conjugating Enzyme Cdc34 and Ubiquitin Ligase Skp1-Cullin-F-box Ligase (SCF) Interact through Multiple Conformations. The Journal of biological chemistry 290:1106–1118.

Harrison JS, Jacobs TM, Houlihan K, Doorslaer KV, Kuhlman B, (2015) UbSRD: The Ubiquitin Structural Relational Database. Journal of Molecular Biology doi:10.1016/j.jmb.2015.09.011.

 

2014

Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B, (2014) Computational de novo design of a four-helix bundle protein-DND_4HB. Protein Science 24:434–445.

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, Demarest SJ, (2014) Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Nature Biotechnology 32:191–198.

Strande NT, Carvajal-Garcia J, Hallett RA, Waters CA, Roberts SA, Strom C, Kuhlman B, Ramsden DA, (2014) Requirements for 5’dRP/AP lyase activity in Ku. Nucleic Acids Research 42:11136–11143.

Carter CW, Li L, Weinreb V, Collier M, Gonzalez-Rivera K, Jimenez-Rodriguez M, Erdogan O, Kuhlman B, Ambroggio X, Williams T, Chandrasekharan S, (2014) 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.

 

2013

Choi EJ, Choi EJ, Jacak R, Jacak R, Kuhlman B, Kuhlman B, (2013) A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins. Protein Engineering Design and Selection 26:283–289.

Drew K, Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou F-C, Chou F-C, Lyskov S, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Pacella M, Kilambi KP, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Gray JJ, Bradley P, Bradley P, Kirshenbaum K, Arora PS, Das R, Das R, Bonneau R, (2013) Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design. PLOS ONE 8:e67051.

Der BS, Der BS, Kluwe C, Kluwe C, Miklos AE, Miklos AE, Jacak R, Jacak R, Lyskov S, Lyskov S, Gray JJ, Gray JJ, Georgiou G, Georgiou G, Ellington AD, Ellington AD, Kuhlman B, (2013) Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability. PLOS ONE 8:e64363.

Der BS, Der BS, Jha RK, Jha RK, Jha RK, Lewis SM, Lewis SM, Thompson PM, Thompson PM, Guntas G, Guntas G, Kuhlman B, (2013) 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: Structure, Function, and Bioinformatics 81:1245–1255.

Harrison JS, Harrison JS, Higgins CD, Higgins CD, O’Meara MJ, O’Meara MJ, Koellhoffer JF, Koellhoffer JF, Kuhlman BA, Kuhlman BA, Lai JR, Lai JR, (2013) Role of Electrostatic Repulsion in Controlling pH-Dependent Conformational Changes of Viral Fusion Proteins. Structure 21:1085–1096.

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, Baker D, Kuhlman B, (2013) Scientific benchmarks for guiding macromolecular energy function improvement. Methods in enzymology 523:109–143.

Lyskov S, Chou F-C, 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, Gray JJ, Das R, (2013) Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PloS one 8:e63906.

Zhang J, Zhang J, Lewis SM, Lewis SM, Kuhlman B, Lee AL, Lee AL, (2013) Supertertiary Structure of the MAGUK Core from PSD-95. Structure 21:402–413.

Jacobs TM, Jacobs TM, Kuhlman B, (2013) Using anchoring motifs for the computational design of protein–protein interactions. Biochemical Society Transactions 41:1141–1145.

 

2012

Stranges PB, Stranges PB, Kuhlman B, (2012) A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Protein Science 22:74–82.

Der BS, Der BS, Edwards DR, Edwards DR, Kuhlman B, (2012) Catalysis by a De Novo Zinc-Mediated Protein Interface: Implications for Natural Enzyme Evolution and Rational Enzyme Engineering. Biochemistry 51:3933–3940.

Lungu OI, Lungu OI, Hallett RA, Hallett RA, Choi EJ, Choi EJ, Aiken MJ, Aiken MJ, Hahn KM, Kuhlman B, (2012) Designing Photoswitchable Peptides Using the AsLOV2 Domain. Chemistry & Biology 19:507–517.

Renfrew PD, Renfrew PD, Choi EJ, Choi EJ, Bonneau R, Kuhlman B, (2012) Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design. PLOS ONE 7:e32637.

Murphy GS, Mills JL, Miley MJ, Machius M, Szyperski T, Kuhlman B, (2012) Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core. Structure (London, England : 1993) 20:1086–1096.

Der BS, Der BS, Machius M, Machius M, Miley MJ, Miley MJ, Mills JL, Mills JL, Szyperski T, Szyperski T, Kuhlman B, (2012) Metal-Mediated Affinity and Orientation Specificity in a Computationally Designed Protein Homodimer. Journal of the American Chemical Society 134:375–385.

Guntas G, Guntas G, Kuhlman B, (2012) Redesigning the NEDD8 Pathway with a Bacterial Genetic Screen for Ubiquitin-Like Molecule Transfer. Journal of Molecular Biology 418:161–166.

Baker R, Baker R, Lewis SM, Lewis SM, Sasaki AT, Sasaki AT, Wilkerson EM, Wilkerson EM, Locasale JW, Locasale JW, Cantley LC, Cantley LC, Kuhlman B, Dohlman HG, Dohlman HG, Campbell SL, Campbell SL, (2012) Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function. Nature Structural & Molecular Biology 20:46–52.

Miklos AE, Miklos AE, Kluwe C, Kluwe C, Der BS, Der BS, Pai S, Sircar A, Sircar A, Hughes RA, Berrondo M, Berrondo M, Xu J, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Gray JJ, Georgiou G, Georgiou G, Kuhlman B, Ellington AD, Ellington AD, (2012) Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies. Chemistry & Biology 19:449–455.

 

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, (2011) A biosensor generated via high-throughput screening quantifies cell edge Src dynamics. Nature Chemical Biology 7:437–444.

Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B, (2011) A Generic Program for Multistate Protein Design. Plos One 6:e20937. PMCID: PMCID:PMC3130737

Leaver-Fay A, Kuhlman B, Snoeyink J, (2011) AN ADAPTIVE DYNAMIC PROGRAMMING ALGORITHM FOR THE SIDE CHAIN PLACEMENT PROBLEM. :16–27.

Lewis SM, Kuhlman BA, (2011) Anchored design of protein-protein interfaces. PloS one 6:e20872.

Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B, (2011) Computational design of a symmetric homodimer using β-strand assembly. Proceedings Of The National Academy Of Sciences Of The United States Of America 108:20562–20567.

Sammond DW, Sammond DW, Bosch DE, Bosch DE, Butterfoss GL, Purbeck C, Purbeck C, Machius M, Machius M, Siderovski DP, Siderovski DP, Kuhlman B, (2011) Computational Design of the Sequence and Structure of a Protein-Binding Peptide. Journal of the American Chemical Society 133:4190–4192.

Jacak R, Jacak R, Leaver-Fay A, Leaver-Fay A, Kuhlman B, (2011) Computational protein design with explicit consideration of surface hydrophobic patches. Proteins: Structure, Function, and Bioinformatics 80:825–838.

Saha A, Saha A, Lewis S, Kleiger G, Kleiger G, Kuhlman B, Deshaies RJ, Deshaies RJ, (2011) Essential Role for Ubiquitin-Ubiquitin-Conjugating Enzyme Interaction in Ubiquitin Discharge from Cdc34 to Substrate. Molecular Cell 42:75–83.

Jha RK, Jha RK, Wu YI, Wu YI, Zawistowski JS, Zawistowski JS, Macnevin C, MacNevin C, Hahn KM, Kuhlman B, (2011) Redesign of the PAK1 Autoinhibitory Domain for Enhanced Stability and Affinity in Biosensor Applications. Journal of Molecular Biology 413:513–522.

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, Ban Y-EA, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P, (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in enzymology 487:545–574.

Bosch DE, Bosch DE, Kimple AJ, Sammond DW, Sammond DW, Muller RE, Miley MJ, Miley MJ, Machius M, Machius M, Kuhlman B, Willard FS, Siderovski DP, (2011) Structural Determinants of Affinity Enhancement between GoLoco Motifs and G-Protein  Subunit Mutants. The Journal of biological chemistry 286:3351–3358.

 

2010

Jha RK, Jha RK, Leaver-Fay A, Leaver-Fay A, Yin S, Yin S, Wu Y, Wu Y, Butterfoss GL, Szyperski T, Szyperski T, Dokholyan NV, Kuhlman B, (2010) Computational Design of a PAK1 Binding Protein. Journal of Molecular Biology 400:257–270.

Purbeck C, Purbeck C, Eletr ZM, Eletr ZM, Kuhlman B, (2010) Kinetics of the Transfer of Ubiquitin from UbcH7 to E6AP. Biochemistry 49:1361–1363.

Salgado EN, Salgado EN, Ambroggio XI, Ambroggio XI, Brodin JD, Brodin JD, Lewis RA, Lewis RA, Kuhlman B, Kuhlman B, Tezcan FA, Tezcan FA, (2010) Metal templated design of protein interfaces. Proceedings of the National Academy of Sciences 107:1827–1832.

Pham Y, Kuhlman B, Butterfoss GL, Hu H, Weinreb V, Carter CW, (2010) Tryptophanyl-tRNA Synthetase Urzyme: A MODEL TO RECAPITULATE MOLECULAR EVOLUTION AND INVESTIGATE INTRAMOLECULAR COMPLEMENTATION. The Journal of biological chemistry 285:38590–38601.

 

2009

Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM, (2009) A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 461:104–108.

Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R, (2009) A Preliminary Survey of the Peptoid Folding Landscape. Journal of the American Chemical Society 131:16798–16807.

Sammond DW, Sammond DW, Eletr ZM, Eletr ZM, Purbeck C, Purbeck C, Kuhlman B, (2009) Computational design of second-site suppressor mutations at protein-protein interfaces. Proteins: Structure, Function, and Bioinformatics 78:1055–1065.

Nauli S, Kuhlman B, Trong IL, Stenkamp RE, Teller D, Baker D, (2009) Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein Science 11:2924–2931.

Torres MP, Lee MJ, Ding F, Purbeck C, Kuhlman B, Dokholyan NV, Dohlman HG, (2009) G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase. The Journal of biological chemistry 284:8940–8950.

Kleiger G, Kleiger G, Saha A, Saha A, Lewis S, Kuhlman B, Deshaies RJ, Deshaies RJ, (2009) Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates. Cell 139:957–968.

 

2008

Hu X, Hu X, Wang H, Wang H, Ke H, Ke H, Kuhlman B, (2008) Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design. Structure 16:1799–1805.

 

2007

Kapustina M, Weinreb V, Li L, Kuhlman B, Jr. CWC, (2007) A Conformational Transition State Accompanies Tryptophan Activation by B. stearothermophilus Tryptophanyl-tRNA Synthetase. Structure 15:1272–1284.

Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL, Kuhlman B, Jr. CWC, (2007) A Minimal TrpRS Catalytic Domain Supports Sense/Antisense Ancestry of Class I and II Aminoacyl-tRNA Synthetases. Molecular Cell 25:851–862.

Hu X, Hu X, Wang H, Wang H, Ke H, Ke H, Kuhlman B, Kuhlman B, (2007) High-resolution design of a protein loop. Proceedings of the National Academy of Sciences 104:17668–17673.

Dantas G, Corrent C, Corrent C, Reichow SL, Reichow SL, Havranek JJ, Havranek JJ, Eletr ZM, Eletr ZM, Isern NG, Isern NG, Kuhlman B, Varani G, Merritt EA, Merritt EA, Baker D, (2007) High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design. Journal of Molecular Biology 366:1209–1221.

Dantas G, Corrent C, Reichow SL, Havranek JJ, Eletr ZM, Isern NG, Kuhlman B, Varani G, Merritt EA, Baker D, (2007) High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design. J Mol Biol 366:1209–1221. PMCID: PMCID:PMC3764424

Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B, (2007) Maintaining solvent accessible surface area under rotamer substitution for protein design. Journal of Computational Chemistry 28:1336–1341.

Eletr ZM, Eletr ZM, Kuhlman B, (2007) Sequence Determinants of E2-E6AP Binding Affinity and Specificity. Journal of Molecular Biology 369:419–428.

Sammond DW, Sammond DW, Eletr ZM, Eletr ZM, Purbeck C, Purbeck C, Kimple RJ, Kimple RJ, Siderovski DP, Siderovski DP, Kuhlman B, (2007) Structure-based Protocol for Identifying Mutations that Enhance Protein–Protein Binding Affinities. Journal of Molecular Biology 371:1392–1404.

Renfrew PD, Renfrew PD, Butterfoss GL, Kuhlman B, (2007) Using quantum mechanics to improve estimates of amino acid side chain rotamer energies. Proteins: Structure, Function, and Bioinformatics 71:1637–1646.

 

2006

Ambroggio XI, Kuhlman B, (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds. Journal of the American Chemical Society 128:1154–1161.

Johnston CA, Lobanova ES, Shavkunov AS, Low J, Ramer JK, Blaesius R, Fredericks Z, Willard FS, Kuhlman B, Arshavsky VY, Siderovski DP, (2006) Minimal Determinants for Binding Activated Gα from the Structure of a Gα i1−Peptide Dimer †,‡. Biochemistry 45:11390–11400.

Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D, (2006) Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution. Journal of Molecular Biology 362:1004–1024.

Liu Y, Kuhlman B, (2006) RosettaDesign server for protein design. Nucleic Acids Research 34:W235–W238.

 

2005

Jiang L, Kuhlman B, Kortemme T, Baker D, (2005) A “solvated rotamer” approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins: Structure, Function, and Bioinformatics 58:893–904.

Eletr ZM, Eletr ZM, Huang DT, Huang DT, Duda DM, Duda DM, Schulman BA, Schulman BA, Kuhlman B, (2005) E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer. Nature Structural & Molecular Biology 12:933–934.

Hu X, Hu X, Kuhlman B, (2005) Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences. Proteins: Structure, Function, and Bioinformatics 62:739–748.

 

2003

Dantas G, Kuhlman B, Callender D, Callender D, Wong M, Wong M, Baker D, (2003) A Large Scale Test of Computational Protein Design: Folding and Stability of Nine Completely Redesigned Globular Proteins. Journal of Molecular Biology 332:449–460.

Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D, (2003) An improved protein decoy set for testing energy functions for protein structure prediction. Proteins: Structure, Function, and Bioinformatics 53:76–87.

Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D, (2003) Design of a Novel Globular Protein Fold with Atomic-Level Accuracy. Science 302:1364–1368.

Gray JJ, Gray JJ, Moughon S, Moughon S, Wang C, Wang C, Schueler-Furman O, Schueler-Furman O, Kuhlman B, Rohl CA, Rohl CA, Baker D, (2003) Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations. Journal of Molecular Biology 331:281–299.

 

2002

Kuhlman B, O’Neill JW, Kim DE, Zhang KYJ, Baker D, (2002) Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of Molecular Biology 315:471–477.

 

2001

Nauli S, Kuhlman B, Baker D, (2001) Computer-based redesign of a protein folding pathway. Nature Structural Biology 8:602–605.

Kuhlman B, O’Neill JW, Kim DE, Zhang KYJ, Baker D, (2001) Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences 98:10687–10691.

 

2000

Kuhlman B, Baker D, (2000) Native protein sequences are close to optimal for their structures. Proc National Acad Sci 97:10383–10388. PMCID: PMCID:PMC27033

 

1999

Luisi DL, Kuhlman B, Sideras K, Evans PA, Raleigh DP, (1999) Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed α/β protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L911Edited by P. E. Wright. J Mol Biol 289:167–174.

Sato S, Kuhlman B, Wu W-J, Raleigh DP, (1999) Folding of the Multidomain Ribosomal Protein L9: The Two Domains Fold Independently with Remarkably Different Rates †. Biochemistry-us 38:5643–5650.

Kuhlman B, Luisi DL, Young P, Raleigh DP, (1999) 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-us 38:4896–903.

 

1998

Vugmeyster L, Kuhlman B, Raleigh DP, (1998) 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 Sci 7:1994–1997. PMCID: PMCID:PMC2144167

Spector S, Kuhlman B, Fairman R, Wong E, Boice JA, Raleigh DP, (1998) Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex11Edited by P. E. Wright. J Mol Biol 276:479–489.

Kuhlman B, Luisi DL, Evans PA, Raleigh DP, (1998) Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L911Edited by P. E. Wright. J Mol Biol 284:1661–1670.

Kuhlman B, Raleigh DP, (1998) 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, ΔH°, ΔS°, and ΔC°p, and evaluation of solvent isotope effects. Protein Sci 7:2405–2412. PMCID: PMCID:PMC2143857

Kuhlman B, Boice JA, Fairman R, Raleigh DP, (1998) Structure and Stability of the N-Terminal Domain of the Ribosomal Protein L9: Evidence for Rapid Two-State Folding †. Biochemistry-us 37:1025–1032.

 

1997

Kuhlman B, Yang HY, Boice JA, Fairman R, Raleigh DP, (1997) An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability11Edited by P. E. Wright. J Mol Biol 270:640–647.

Kuhlman B, Boice JA, Wu W-J, Fairman R, Raleigh DP, (1997) Calcium Binding Peptides from α-Lactalbumin: Implications for Protein Folding and Stability †. Biochemistry-us 36:4607–4615.