Year |
Citation |
Score |
2023 |
Chu AE, Cheng L, El Nesr G, Xu M, Huang PS. An all-atom protein generative model. Biorxiv : the Preprint Server For Biology. PMID 37292974 DOI: 10.1101/2023.05.24.542194 |
0.382 |
|
2022 |
Chu AE, Fernandez D, Liu J, Eguchi RR, Huang PS. De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design. Biodesign Research. 2022: 9842315. PMID 37850141 DOI: 10.34133/2022/9842315 |
0.443 |
|
2022 |
Eguchi RR, Choe CA, Huang PS. Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation. Plos Computational Biology. 18: e1010271. PMID 35759518 DOI: 10.1371/journal.pcbi.1010271 |
0.401 |
|
2022 |
Ren J, Chu AE, Jude KM, Picton LK, Kare AJ, Su L, Montano Romero A, Huang PS, Garcia KC. Interleukin-2 superkines by computational design. Proceedings of the National Academy of Sciences of the United States of America. 119: e2117401119. PMID 35294290 DOI: 10.1073/pnas.2117401119 |
0.335 |
|
2022 |
Anand N, Eguchi R, Mathews II, Perez CP, Derry A, Altman RB, Huang PS. Protein sequence design with a learned potential. Nature Communications. 13: 746. PMID 35136054 DOI: 10.1038/s41467-022-28313-9 |
0.423 |
|
2021 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Correction to 'Theoretical basis for stabilizing messenger RNA through secondary structure design'. Nucleic Acids Research. PMID 34591967 DOI: 10.1093/nar/gkab911 |
0.48 |
|
2021 |
Ovchinnikov S, Huang PS. Structure-based protein design with deep learning. Current Opinion in Chemical Biology. 65: 136-144. PMID 34547592 DOI: 10.1016/j.cbpa.2021.08.004 |
0.69 |
|
2021 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Watkins AM, Parra Sperberg RA, Huang PS, Participants E, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Nucleic Acids Research. PMID 34520542 DOI: 10.1093/nar/gkab764 |
0.507 |
|
2020 |
Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjöström HS, Hilvert D, Baker D, Zeymer C. Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Proceedings of the National Academy of Sciences of the United States of America. PMID 33203677 DOI: 10.1073/pnas.2008535117 |
0.792 |
|
2020 |
Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Sperberg RAP, Huang PS, Das R. Theoretical basis for stabilizing messenger RNA through secondary structure design. Biorxiv : the Preprint Server For Biology. PMID 32869022 DOI: 10.1101/2020.08.22.262931 |
0.468 |
|
2020 |
Xu C, Lu P, Gamal El-Din TM, Pei XY, Johnson MC, Uyeda A, Bick MJ, Xu Q, Jiang D, Bai H, Reggiano G, Hsia Y, Brunette TJ, Dou J, Ma D, ... ... Huang PS, et al. Computational design of transmembrane pores. Nature. PMID 32848250 DOI: 10.1038/S41586-020-2646-5 |
0.794 |
|
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, ... ... Huang PS, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.564 |
|
2020 |
Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188784 DOI: 10.1073/Pnas.1914808117 |
0.725 |
|
2019 |
Huang PS, Thompson KA. Harnessing Human Neural Networks for Protein Design. Biochemistry. PMID 31834781 DOI: 10.1021/Acs.Biochem.9B00820 |
0.36 |
|
2019 |
Meier S, Bohnacker S, Klose CJ, Lopez A, Choe CA, Schmid PWN, Bloemeke N, Rührnößl F, Haslbeck M, Bieren JE, Sattler M, Huang PS, Feige MJ. The molecular basis of chaperone-mediated interleukin 23 assembly control. Nature Communications. 10: 4121. PMID 31511508 DOI: 10.1038/S41467-019-12006-X |
0.343 |
|
2019 |
Eguchi RR, Huang PS. Multi-Scale Structural Analysis of Proteins by Deep Semantic Segmentation. Bioinformatics (Oxford, England). PMID 31424530 DOI: 10.1093/Bioinformatics/Btz650 |
0.434 |
|
2018 |
Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, et al. De novo design of a fluorescence-activating β-barrel. Nature. PMID 30209393 DOI: 10.1038/S41586-018-0509-0 |
0.79 |
|
2017 |
Parmeggiani F, Huang PS. Designing repeat proteins: a modular approach to protein design. Current Opinion in Structural Biology. 45: 116-123. PMID 28267654 DOI: 10.1016/J.Sbi.2017.02.001 |
0.544 |
|
2017 |
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Protein structure determination using metagenome sequence data. Science (New York, N.Y.). 355: 294-298. PMID 28104891 DOI: 10.1126/Science.Aah4043 |
0.693 |
|
2016 |
Rose JC, Huang PS, Camp ND, Ye J, Leidal AM, Goreshnik I, Trevillian BM, Dickinson MS, Cunningham-Bryant D, Debnath J, Baker D, Wolf-Yadlin A, Maly DJ. A computationally engineered RAS rheostat reveals RAS-ERK signaling dynamics. Nature Chemical Biology. PMID 27870838 DOI: 10.1038/Nchembio.2244 |
0.385 |
|
2016 |
Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Corrigendum: Design of a hyperstable 60-subunit protein icosahedron. Nature. PMID 27760110 DOI: 10.1038/Nature20108 |
0.777 |
|
2016 |
Huang PS, Boyken SE, Baker D. The coming of age of de novo protein design. Nature. 537: 320-327. PMID 27629638 DOI: 10.1038/Nature19946 |
0.514 |
|
2016 |
Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, et al. Accurate de novo design of hyperstable constrained peptides. Nature. PMID 27626386 DOI: 10.1038/Nature19791 |
0.752 |
|
2016 |
Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D. Design of a hyperstable 60-subunit protein icosahedron. Nature. PMID 27309817 DOI: 10.1038/Nature18010 |
0.804 |
|
2015 |
Brunette TJ, Parmeggiani F, Huang PS, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Exploring the repeat protein universe through computational protein design. Nature. PMID 26675729 DOI: 10.1038/Nature16162 |
0.543 |
|
2015 |
Huang PS, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Höcker B, Baker D. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nature Chemical Biology. PMID 26595462 DOI: 10.1038/Nchembio.1966 |
0.606 |
|
2015 |
Mou Y, Huang PS, Hsu FC, Huang SJ, Mayo SL. Computational design and experimental verification of a symmetric protein homodimer. Proceedings of the National Academy of Sciences of the United States of America. 112: 10714-9. PMID 26269568 DOI: 10.1073/Pnas.1505072112 |
0.721 |
|
2015 |
Mou Y, Huang PS, Thomas LM, Mayo SL. Using molecular dynamics simulations as an aid in the prediction of domain swapping of computationally designed protein variants. Journal of Molecular Biology. PMID 26101839 DOI: 10.1016/J.Jmb.2015.06.006 |
0.655 |
|
2015 |
Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nature Structural & Molecular Biology. 22: 167-74. PMID 25580576 DOI: 10.1038/Nsmb.2938 |
0.513 |
|
2015 |
Kaltofen S, Li C, Huang PS, Serpell LC, Barth A, André I. Computational de novo design of a self-assembling peptide with predefined structure. Journal of Molecular Biology. 427: 550-62. PMID 25498388 DOI: 10.1016/J.Jmb.2014.12.002 |
0.681 |
|
2015 |
Parmeggiani F, Huang PS, Vorobiev S, Xiao R, Park K, Caprari S, Su M, Seetharaman J, Mao L, Janjua H, Montelione GT, Hunt J, Baker D. A general computational approach for repeat protein design. Journal of Molecular Biology. 427: 563-75. PMID 25451037 DOI: 10.1016/J.Jmb.2014.11.005 |
0.522 |
|
2015 |
Mou Y, Huang P, Hsu F, Huang S, Mayo S. Solution structure of a computational designed dimer based on the engrailed homeodomain structure Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr19585 |
0.39 |
|
2014 |
Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D. High thermodynamic stability of parametrically designed helical bundles. Science (New York, N.Y.). 346: 481-5. PMID 25342806 DOI: 10.1126/Science.1257481 |
0.725 |
|
2011 |
Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR. Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science (New York, N.Y.). 334: 373-6. PMID 22021856 DOI: 10.1126/Science.1209368 |
0.43 |
|
2011 |
Huang PS, Ban YE, Richter F, Andre I, Vernon R, Schief WR, Baker D. RosettaRemodel: a generalized framework for flexible backbone protein design. Plos One. 6: e24109. PMID 21909381 DOI: 10.1371/Journal.Pone.0024109 |
0.818 |
|
2011 |
Correia BE, Holmes MA, Huang PS, Strong RK, Schief WR. High-resolution structure prediction of a circular permutation loop. Protein Science : a Publication of the Protein Society. 20: 1929-34. PMID 21898647 DOI: 10.1002/Pro.725 |
0.49 |
|
2007 |
Huang PS, Love JJ, Mayo SL. A de novo designed protein protein interface. Protein Science : a Publication of the Protein Society. 16: 2770-4. PMID 18029425 DOI: 10.1110/Ps.073125207 |
0.684 |
|
2005 |
Huang PS, Love JJ, Mayo SL. Adaptation of a fast Fourier transform-based docking algorithm for protein design. Journal of Computational Chemistry. 26: 1222-32. PMID 15962277 DOI: 10.1002/Jcc.20252 |
0.675 |
|
2004 |
Shukla UJ, Marino H, Huang PS, Mayo SL, Love JJ. A designed protein interface that blocks fibril formation. Journal of the American Chemical Society. 126: 13914-5. PMID 15506739 DOI: 10.1021/Ja0456858 |
0.637 |
|
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