| Year |
Citation |
Score |
| 2023 |
Guffy SL, Pulavarti SVSRK, Harrison J, Fleming D, Szyperski T, Kuhlman B. Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry. PMID 36634348 DOI: 10.1021/acs.biochem.2c00595 |
0.716 |
|
| 2022 |
Thieker DF, Maguire JB, Kudlacek ST, Leaver-Fay A, Lyskov S, Kuhlman B. Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein Science : a Publication of the Protein Society. 31: e4428. PMID 36173174 DOI: 10.1002/pro.4428 |
0.686 |
|
| 2022 |
Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B. AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein Science : a Publication of the Protein Society. 31: e4368. PMID 35762713 DOI: 10.1002/pro.4368 |
0.803 |
|
| 2022 |
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. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500 |
0.781 |
|
| 2022 |
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. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. The Journal of Physical Chemistry. B. PMID 35128921 DOI: 10.1021/acs.jpcb.1c10750 |
0.69 |
|
| 2022 |
Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. Journal of the American Chemical Society. PMID 35108000 DOI: 10.1021/jacs.1c09902 |
0.644 |
|
| 2021 |
Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, ... ... Kuhlman B, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147 |
0.791 |
|
| 2021 |
Koehler Leman J, 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, ... ... Kuhlman B, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7 |
0.776 |
|
| 2021 |
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, ... ... Kuhlman B, et al. Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Science Advances. 7: eabg4084. PMID 34652943 DOI: 10.1126/sciadv.abg4084 |
0.778 |
|
| 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 |
0.428 |
|
| 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 |
0.348 |
|
| 2020 |
Stone OJ, Pankow N, Liu B, Sharma VP, Eddy RJ, Wang H, Putz AT, Teets FD, Kuhlman B, Condeelis JS, Hahn KM. Author Correction: Optogenetic control of cofilin and αTAT in living cells using Z-lock. Nature Chemical Biology. PMID 32694868 DOI: 10.1038/S41589-020-0614-X |
0.755 |
|
| 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 |
0.742 |
|
| 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 |
0.778 |
|
| 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 |
0.542 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009 |
0.74 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008 |
0.756 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007 |
0.744 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005 |
0.732 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004 |
0.74 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003 |
0.758 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002 |
0.747 |
|
| 2020 |
Leman JK, 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, Schueler-Furman O, ... ... Kuhlman B, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001 |
0.734 |
|
| 2020 |
Maillie C, Thanh Phanh T, Kuhlman B. Computational Design of a Stable DIII Pentamer of Dengue Virus Envelope Protein as an Immunogen with Rosetta Biophysical Journal. 118: 45a. DOI: 10.1016/J.Bpj.2019.11.427 |
0.325 |
|
| 2019 |
Teets FD, Watanabe T, Hahn KM, Kuhlman B. A computational protocol for regulating protein binding reactions with a light sensitive protein dimer. Journal of Molecular Biology. PMID 31887287 DOI: 10.1016/J.Jmb.2019.12.033 |
0.796 |
|
| 2019 |
Stone OJ, Pankow N, Liu B, Sharma VP, Eddy RJ, Wang H, Putz AT, Teets FD, Kuhlman B, Condeelis JS, Hahn KM. Optogenetic control of cofilin and αTAT in living cells using Z-lock. Nature Chemical Biology. 15: 1183-1190. PMID 31740825 DOI: 10.1038/S41589-019-0405-4 |
0.782 |
|
| 2019 |
Kuhlman B. Designing protein structures and complexes with the molecular modeling program Rosetta. The Journal of Biological Chemistry. PMID 31699898 DOI: 10.1074/Jbc.Aw119.008144 |
0.423 |
|
| 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 |
0.614 |
|
| 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 |
0.306 |
|
| 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 |
0.637 |
|
| 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 |
0.403 |
|
| 2018 |
Hussain M, Angus SP, Kuhlman B. Engineering a Protein Binder Specific for p38α with Interface Expansion. Biochemistry. PMID 29975520 DOI: 10.1021/Acs.Biochem.8B00408 |
0.335 |
|
| 2018 |
Kudlacek ST, Premkumar L, Metz SW, Tripathy A, Bobkov AA, Payne AM, Graham S, Brackbill JA, Miley MJ, de Silva AM, Kuhlman B. Physiological temperatures reduce dimerization of dengue and Zika virus recombinant envelope proteins. The Journal of Biological Chemistry. PMID 29678884 DOI: 10.1074/Jbc.Ra118.002658 |
0.744 |
|
| 2018 |
Guffy SL, Teets FD, Langlois MI, Kuhlman B. Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program. Journal of Chemical Information and Modeling. PMID 29659276 DOI: 10.1021/Acs.Jcim.8B00060 |
0.819 |
|
| 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 |
0.349 |
|
| 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 |
0.663 |
|
| 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 |
0.338 |
|
| 2018 |
Bonner X, Kuhlman B, Yumerefendi H. Analysis of Relative Binding Affinity Predictions for Protein-Protein Complexes Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.2262 |
0.318 |
|
| 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 |
0.694 |
|
| 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 |
0.794 |
|
| 2017 |
Alford RF, Leaver-Fay A, Jeliazkov JR, Pacella MS, Kuhlman B, Kortemme T, Gray JJ. A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1078 |
0.794 |
|
| 2016 |
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. 291: 23830-23831. PMID 27815453 DOI: 10.1074/jbc.A115.642876 |
0.664 |
|
| 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 |
0.661 |
|
| 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 |
0.329 |
|
| 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 |
0.391 |
|
| 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 |
0.674 |
|
| 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 |
0.401 |
|
| 2016 |
Kuhlman B, Jacobs T, Linskey T. Computational Design of Protein Linkers. Methods in Molecular Biology (Clifton, N.J.). 1414: 341-51. PMID 27094301 DOI: 10.1007/978-1-4939-3569-7_20 |
0.396 |
|
| 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 |
0.702 |
|
| 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 |
0.71 |
|
| 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 |
0.75 |
|
| 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. Author response: Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1 Elife. DOI: 10.7554/Elife.17101.024 |
0.645 |
|
| 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 |
0.362 |
|
| 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 |
0.662 |
|
| 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 |
0.335 |
|
| 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 |
0.317 |
|
| 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 |
0.711 |
|
| 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 |
0.705 |
|
| 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 |
0.774 |
|
| 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 |
0.654 |
|
| 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 |
0.315 |
|
| 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 |
0.309 |
|
| 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 |
0.42 |
|
| 2015 |
Eletsky A, Federizon J, Xu X, Pulavarti SVSRK, Jacobs T, Kuhlman B, Szyperski T. Solution NMR Structure of Designed Protein DA05R1, Northeast Structural Genomics Consortium (NESG) Target OR690 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr25868 |
0.309 |
|
| 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 |
0.715 |
|
| 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 |
0.682 |
|
| 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 |
0.417 |
|
| 2013 |
Der BS, Kuhlman B. Cages from coils. Nature Biotechnology. 31: 809-10. PMID 24022157 DOI: 10.1038/Nbt.2670 |
0.358 |
|
| 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 |
0.655 |
|
| 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 |
0.82 |
|
| 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 |
0.78 |
|
| 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 |
0.469 |
|
| 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 |
0.371 |
|
| 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 |
0.805 |
|
| 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.24280 |
0.367 |
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| 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 |
0.766 |
|
| 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 |
0.345 |
|
| 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 |
0.4 |
|
| 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. Author response: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3 Elife. DOI: 10.7554/Elife.00828.023 |
0.651 |
|
| 2013 |
Der BS, Jha RK, Lewis SM, Thompson PM, Guntas G, Kuhlman B. Erratum to Originally published in PROTEINS: Structure, Function, and Bioinformatics [81(7), (2013), 1245-1255] DOI:10.1002/prot.24280 Proteins. 81: 1678-1679. DOI: 10.1002/Prot.24379 |
0.325 |
|
| 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 |
0.39 |
|
| 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 |
0.565 |
|
| 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 |
0.341 |
|
| 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 |
0.567 |
|
| 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 |
0.719 |
|
| 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 |
0.375 |
|
| 2012 |
Xu J, Miklos AE, Hughes R, Kuhlman B, Georgiou G, Ellington AD, Gray JJ. A Systematic Computational Method to Predict and Enhance Antibody-Antigen Binding in the Absence of Antibody Crystal Structures Biophysical Journal. 102: 621a. DOI: 10.1016/J.Bpj.2011.11.3382 |
0.559 |
|
| 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 |
0.816 |
|
| 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 |
0.71 |
|
| 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 |
0.379 |
|
| 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 |
0.538 |
|
| 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 |
0.346 |
|
| 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 |
0.768 |
|
| 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 |
0.334 |
|
| 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 |
0.712 |
|
| 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 |
0.724 |
|
| 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 |
0.351 |
|
| 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 |
0.557 |
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| 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 |
0.496 |
|
| 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 |
0.406 |
|
| 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 |
0.681 |
|
| 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 |
0.303 |
|
| 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 |
0.378 |
|
| 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 |
0.35 |
|
| 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 |
0.76 |
|
| 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 |
0.313 |
|
| 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 |
0.345 |
|
| 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 |
0.778 |
|
| 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 |
0.752 |
|
| 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 |
0.803 |
|
| 2006 |
Liu Y, Kuhlman B. RosettaDesign server for protein design. Nucleic Acids Research. 34: W235-8. PMID 16845000 DOI: 10.1093/Nar/Gkl163 |
0.4 |
|
| 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 |
0.746 |
|
| 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 |
0.414 |
|
| 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 |
0.732 |
|
| 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 |
0.357 |
|
| 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 |
0.727 |
|
| 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 |
0.697 |
|
| 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 |
0.729 |
|
| 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 |
0.484 |
|
| 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 |
0.621 |
|
| 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 |
0.645 |
|
| 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 |
0.799 |
|
| 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 |
0.802 |
|
| 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 |
0.693 |
|
| 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 |
0.462 |
|
| 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 |
0.432 |
|
| 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 |
0.681 |
|
| 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 DOI: 10.1073/Pnas.97.19.10383 |
0.43 |
|
| 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 |
0.314 |
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