Possu Huang Lab
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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 & Preprints

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).
  • ​[Full Text PDF]

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).
  • ​[Full Text PDF]   [Supplement]

Ig-VAE: Generative Modeling of Immunoglobulin Proteins by Direct 3D Coordinate Generation​.
Eguchi RR, Choe CA, Huang PS. PLOS Comp Bio (2022).​
  • ​[Full Text PDF]   [Supplement]

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).
  • [Full Text PDF]   [Supplement]

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).
  • [Full Text PDF]

Protein sequence design with a learned potential
Anand N, Eguchi RR, Mathews II, Perez CP, Derry A, Altman RB, Huang PS. Nature Communications (2022).​
  • ​[Full Text PDF]
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​​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).
  • ​[Full Text PDF]   [Supplement]

Structure-based protein design with deep learning
Ovchinnikov S, Huang PS. Current Opinion in Chemical Biology (2021)
  • ​[Full Text PDF]

​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).​
  • [Full Text PDF]    [Supplement]    [PubMed]

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).​
  • [Full Text PDF]    [Supplement]

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).​
  • ​[Full Text PDF]   [Supplement]

​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).​
  • [Full Text PDF]   ​[bioRxiv]   [NeurIPS Talk]

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).​
  • ​[Full Text PDF]   [Supplement]

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).​
  • ​[Full Text PDF]

​Engineering a potent receptor superagonist or antagonist from a novel IL-6 family cytokine ligand.
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Kim JW, Marquez CP, Sperberg RAP, Wu J, Bae WG, Huang PS, Sweet-Cordero EA†, Cochran JR†. PNAS (2020).
  • ​[Full Text PDF]   [Supplement]

Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK†, Weitzner BD, Lewis SM, ... , Huang PS, ... , Bonneau R. Nature Methods (2020).
  • ​[Full Text PDF]   [Supplement]

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).
  • [Full Text PDF]   [Supplement]   ​[bioRxiv]​​

Harnessing Human Neural Networks for Protein Design.
Huang PS, Thompson KA. Biochemistry (2019).
  • ​[Full Text PDF]   [PubMed]

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).
  • ​[Full Text PDF]   [Supplement]   [PubMed]
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​​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).
  • [Full Text PDF]   [Supplement]   [PubMed]   ​​[bioRxiv]​
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Multi-Scale Structural Analysis of Proteins by Deep Semantic Segmentation.
Eguchi RR, Huang PS. Bioinformatics (2019).​
  • [Full Text PDF] ​​​  [Supplement]   [PubMed]   [bioRxiv]​​

Fully differentiable full-atom protein backbone generation.
Anand N, Eguchi RR, Huang PS. in ICLR (2019).
  • [Full Text PDF]

​Generative modeling for protein structures.
Anand N, Huang PS. in NeurIPS (2018).
  • [NeurIPS 2018]   ​[ICLR 2018]   [Full Text PDF]   [Supplement]
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​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).
  • [Full Text PDF]   [Supplement]   ​​[PubMed]

​​​​Designing repeat proteins: a modular approach to protein design.
Parmeggiani F, Huang PS. Current Opinion in Structural Biology (2017). ​
  • [Full Text PDF]   [PubMed]

Selected Publications, before Stanford

​​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).​
  • F1000Prime Recommendation
[PubMed]
[Full Text PDF]
The coming of age of de novo protein design.
Huang PS*, Boyken SE*, Baker D*. Nature (2016).
  • ​F1000Prime Recommendation
[PubMed]
[Full Text PDF]
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).
  • ​F1000Prime Recommendation​
[PubMed]
[Full Text PDF]
​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).
  • F1000Prime Recommendation
[PubMed]
[Full Text PDF]
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).
[PubMed]
[Full Text PDF]
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).
  • F1000Prime Recommendation
[PubMed]
[Full Text PDF]
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).​
[PubMed]
[Full Text PDF]
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