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Po-Ssu Huang, Ph.D. - Publications

Affiliations: 
2004 California Institute of Technology, Pasadena, CA 
Area:
Structural Biology
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39 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
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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