See publications on Google Scholar or PubMed.FYI: goes by Possu colloquially, but publishes as Po-Ssu Huang or Po Ssu Huang.
underline = lab members inc. Possu; * = equal contribution; † = co-corresponding authors |
Publications & PreprintsSidechain conditioning and modeling for full-atom protein structure design with FAMPNN
Shuai R*, Widatalla T*, Huang PS, Hie B. bioRxiv (2025) Assessing Generative Model Coverage of Protein Structures with SHAPES Lu T, Liu M, Chen Y, Kim J, Huang PS. bioRxiv (2025) Targeting peptide antigens using multi allelic MHC I-binding system Du H*, Malik L, Hwang D, Sun Y, Kaku C, Hoces D, Sun SM, Carro SD, Phan HAT, Gupta S, Blackson W, Lee H, Choe CA, Dersh D, Liu J, Bell B, Yang H, Papdaki GF, Young MC, Zhou E, El Nesr G, Dasteh K, Eisenlohr LC, Minn AJ, Hernandez-Lopez RA, Jardine JG, Sgourakis NG, Huang PS. Nature Biotechnology (2024) A general platform for targeting MHC-II antigen via a single loop. Du H*, Liu J*, Jude KM, Yang X, Li Y, Bell B, Yang Y, Kassardjian A, Blackson W, Mobedi A, Parekh U, Sperberg RAP, Julien JP, Mellins ED, Garcia KC, Huang PS. Nature Biotechnology (2024).
An all-atom protein generative model. Chu AE, Kim J, Cheng L, El Nesr G, Xu M, Shuai RW, Huang PS. PNAS (2024). Sparks of function by de novo protein design. Chu AE, Lu T, Huang PS. Nature Biotechnology (2024). Full synthetic platform to rapidly generate tetravalent bispecific nanobody-based immunoglobulins Mindrebo LM, Liu H, Ozorowski G, Tran Q, Woehl J, Khalek I, Smith JM, Barman S, Zhao F, Keating C, Limbo O, Verma M, Liu J, Stanfield RL, Zhu X, Turner HL, Sok D, Huang PS Burton DR, Ward AB, Wilson IA, Jardine JG. PNAS (2023). Deep Generative Design of Epitope-Specific Binding Proteins by Latent Conformation Optimization Eguchi RR, Choe CA, Parekh U, Khalek IS, Ward MD, Vithani N, Bowman GR, Jardine JG, Huang PS. bioRxiv (2022). De Novo Design of a Highly Stable TIM Barrel: Unlocking Pocket Shape towards Functional Design Chu AE, Fernandez D, Liu J, Eguchi RR, Huang PS. BioDesign Research (2022).
Ig-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation. Eguchi RR, Choe CA, Huang PS. PLOS Comp Bio (2022).
Interleukin-2 superkines by computational design. Ren J*, Chu AE*, Jude KM*, Picton L, Kare AJ, Su L, Montano Romero A, Huang PS†, Garcia KC†. PNAS (2022). Chimeric mutants of staphylococcal hemolysin, which act as both one‐component and two‐component hemolysin, created by grafting the stem domain Ghanem N, Kanagami N, Matsui T, Takeda K, Kaneko J, Shiraishi Y, Choe CA, Uchikubo-Kamo T, Shirouzu M, Hashimoto T, Ogawa T, Matsuura T, Huang PS, Yokoyama T, Tanaka Y. FEBS journal (2022). Protein sequence design with a learned potential Anand N, Eguchi RR, Mathews II, Perez CP, Derry A, Altman RB, Huang PS. Nature Communications (2022). Theoretical basis for stabilizing messenger RNA through secondary structure design. Wayment-Steele HK, Kim DS, Choe CA, Nicol JJ, Wellington-Oguri R, Sperberg RAP, Huang PS, Eterna Participants, Das R. Nucleic Acids Research (2021). Structure-based protein design with deep learning Ovchinnikov S, Huang PS. Current Opinion in Chemical Biology (2021) Optical control of fast and processive engineered myosins in vitro and in living cells. Ruijgrok PV*, Ghosh RP*, Zemsky S, Nakamura M, Gong R, Ning L, Chen R, Vachharajani VT, Chu AE, Anand N, Eguchi RR, Huang PS, Lin MZ, Alushin GM, Liphardt JT, Bryant Z. Nature Chemical Biology (2021). Identification of N‑Terminally Diversified GLP-1R Agonists Using Saturation Mutagenesis and Chemical Design. Longwell CK, Hanna S, Hartrampf N, Sperberg RAP, Huang PS, Pentelute BL, Cochran JR. ACS Chemical Biology (2021). Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion. Caldwell SJ, Haydon IC, Piperidou N, Huang PS, Bick MJ, Sjöström HS, Hilvert D, Baker D†, Zeymer C†. PNAS (2020). ProGen: Language modeling for protein generation. Madani A, McCann B, Naik N, Keskar NS, Anand N, Chu AE, Eguchi RR, Huang PS, Socher R. NeurIPS, MLSB Workshop (2020). HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors. Lin YR*, Parks KR*, Weidle C, Naidu AS, Khechaduri A, Riker AO, Takushi B, Chun JH, Borst AJ, Veesler D, Stuart A, Agrawal P, Gray M, Pancera M†, Huang PS†, Stamatatos L†. Immunity (2020). Computational design of transmembrane pores. Xu C*, Lu P*†, El-Din TMG, Pei XY, Johnson MC, Uyeda A, Bick MJ, Xu Q, Jiang D, Bai H, Reggiano G, Hsia Y, Brunette TJ, Dou J, Ma D, Lynch EM, Boyken SE, Huang PS, Stewart L, Dimaio F, Kollman JM, Luisi BF, Matsuura T, Catterall WA†, Baker DB†. Nature (2020). Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand. Kim JW, Marquez CP, Sperberg RAP, Wu J, Bae WG, Huang PS, Sweet-Cordero EA†, Cochran JR†. PNAS (2020). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Leman JK†, Weitzner BD, Lewis SM, ... , Huang PS, ... , Bonneau R. Nature Methods (2020). De novo design of proteins with two isoenergetic but structurally divergent ground states. Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE†, Baker D†. PNAS (2020). Harnessing Human Neural Networks for Protein Design. Huang PS, Thompson KA. Biochemistry (2019). The molecular basis of chaperone-mediated interleukin 23 assembly control. Meier S, Bohnacker S, Klose CJ, Lopez A, Choe CA, Schmid PWN, Bloemeke N, Rührnößl F, Haslbeck M, Esser-von Bieren J, Sattler M, Huang PS, Feige MJ. Nature Communications (2019). Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation. Mehta N, Maddineni S, Mathews II, Sperberg RAP, Huang PS†, Cochran JR†. Cell Reports (2019). Multi-Scale Structural Analysis of Proteins by Deep Semantic Segmentation. Eguchi RR, Huang PS. Bioinformatics (2019). Fully differentiable full-atom protein backbone generation. Anand N, Eguchi RR, Huang PS. in ICLR (2019). Generative modeling for protein structures. Anand N, Huang PS. in NeurIPS (2018). De novo design of a fluorescence-activating β-barrel. Dou JY*, Vorobieva AA*, Sheffler W, Doyle LA, Park H, Bick MJ, Mao BC, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D. Nature (2018). Designing repeat proteins: a modular approach to protein design. Parmeggiani F, Huang PS. Current Opinion in Structural Biology (2017). |
Selected Publications, before Stanford
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Protein structure determination using metagenome sequence data.
Ovchinnikov S, Park H, Varghese N, Huang PS, Pavlopoulos GA, Kim DE, Kamisetty H, Kyrpides NC, Baker D. Science (2017). |
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De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
Huang PS, Feldmeier K, Parmeggiani F, Velasco DAF, Höcker B, Baker D. Nature Chemical Biology (2016). |
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Exploring the repeat protein universe through computational protein design.
Brunette TJ*, Parmeggiani F*, Huang PS*, Bhabha G, Ekiert DC, Tsutakawa SE, Hura GL, Tainer JA, Baker D. Nature (2015). |
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High thermodynamic stability of parametrically designed helical bundles.
Huang PS*, Oberdorfer G*, Xu C*, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D. Science (2014). |
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A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield.
Pejchal R*, Doores KJ*, Walker LM*, Khayat R*, Huang PS*, Wang SK, Stanfield RL, Julien JP, Ramos A, Crispin M, Depetris R, Katpally U, Marozsan A, Cupo A, Maloveste S, Liu Y, McBride R, Ito Y, Sanders RW, Ogohara C, Paulson JC, Feizi T, Scanlan CN, Wong CH, Moore JP, Olson WC, Ward AB, Poignard P, Schief WR, Burton DR†, Wilson IA†. Science (2011). |
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RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design.
Huang PS, Ban YA, Richter F, Andre I, Vernon R, Schief WR†, Baker D†. PLoS ONE (2011). |
