research articles
Recent Preprints
Inverse folding of protein complexes with a structure-informed language model enables unsupervised antibody evolution.
Varun R. Shanker, Theodora U.J. Bruun, Brian L. Hie, Peter S. Kim. https://doi.org/10.1101/2023.12.19.572475 bioRxiv (2023).
PUBLICATIONS
2024
145. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. (PDF) (JEM)
Timothy Ting-Hsuan Wu, Kyle J. Travaglini, Arjun Rustagi, Duo Xu, Yue Zhang, Leonid Andronov, SoRi Jang, Astrid Gillich, Roozbeh Dehghannasiri, Giovanny J. Martínez-Colón, Aimee Beck, Daniel Dan Liu, Aaron J. Wilk, Maurizio Morri, Winston L. Trope, Rob Bierman, Irving L. Weissman, Joseph B. Shrager, Stephen R. Quake, Christin S. Kuo, Julia Salzman, W.E. Moerner, Peter S. Kim, Catherine A. Blish, Mark A. Krasnow. J Exp Med (2024) 221 (6): e20232192. doi.org/10.1084/jem.20232192.
144. Design of universal Ebola virus vaccine candidates via immunofocusing. (PDF) (PNAS)
Duo Xu, Abigail E. Powell, Ashley Utz, Mrinmoy Sanyal, Jonathan Do, J. J. Patten, Juan I. Moliva, Nancy J. Sullivan, Robert A. Davey, Peter S. Kim. Proc. Natl. Acad. Sci. USA (2024). doi.org/10.1073/pnas.2316960121.
143. Vaccine design via antigen reorientation. (PDF) (Nat. Chem. Bio)
Duo Xu, Joshua J. Carter, Chunfeng Li, Ashley Utz, Payton A. B. Weidenbacher, Shaogeng Tang, Mrinmoy Sanyal, Bali Pulendran, Christopher O. Barnes, Peter S. Kim. Nature Chemical Biology (2024). doi.org/10.1038/s41589-023-01529-6.
142. Bringing immunofocusing into focus. (PDF) (npj Vaccines)
Sriharshita Musunuri, Payton A. B. Weidenbacher, Peter S. Kim. npj Vaccines (2024). doi.org/10.1038/s41541-023-00792-x.
2023
141. Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines. (PDF) (Vaccine)
Ozan Kumru, Mrinmoy Sanyal, Natalia Friedland, John Hickey, Richa Joshi, Payton Weidenbacher, Jonathan Do, Ya-Chen Cheng, Peter S. Kim, Sangeeta B Joshi, David B Volkin. Vaccine (2023). doi.org/10.1016/j.vaccine.2023.08.037.
140. Efficient evolution of human antibodies from general protein language models. (PDF) (Nat. Bio.)
Brian L. Hie, Varun R. Shanker, Duo Xu, Theodora U. J. Bruun, Payton A. Weidenbacher, Shaogeng Tang, Wesley Wu, John E. Pak, Peter S. Kim. Nature Biotechnology (2023). doi.org/10.1038/s41587-023-01763-2.
139. A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates. (PDF) (Nat. Com.)
Payton A.-B. Weidenbacher, Mrinmoy Sanyal, Natalia Friedland, Shaogeng Tang, Prabhu S. Arunachalam, Mengyun Hu, Ozan S. Kumru, Mary Kate Morris, Jane Fontenot, Lisa Shirreff, Jonathan Do, Ya-Chen Cheng, Gayathri Vasudevan, Mark B. Feinberg, Francois J. Villinger, Carl Hanson, Sangeeta B. Joshi, David B. Volkin, Bali Pulendran, Peter S. Kim. Nature Communications (2023). 2022 Dec 26:2022.12.25.521784. doi: 10.1101/2022.12.25.521784.
138. Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies. (PDF) (J. Bio. Chem.)
Theodora U. J. Bruun, Shaogeng Tang, Graham Erwin, Lindsay Deis, Daniel Fernandez, Peter S. Kim. Journal of Biological Chemistry (2023). doi: 10.1016/j.jbc.2023.103062.
2022
136. Enhancing HIV-1 Neutralization by Increasing the Local Concentration of Membrane-Proximal External Region-Directed Broadly Neutralizing Antibodies. (PDF) (J Virol.)
Soohyun Kim, Maria V. Filsinger Interrante, Peter S. Kim. J Virol. (2022) 10.1128/jvi.01647-22.
134. Converting non-neutralizing SARS-CoV-2 antibodies targeting conserved epitopes into broad-spectrum inhibitors through receptor blockade. (PDF) (Nat. Chem. Bio.)
Payton A.-B. Weidenbacher, Eric Waltari, Izumi de los Rios Kobara, Benjamin N. Bell, John E. Pak, Peter S. Kim. Nature Chemical Biology (2022).
133. Multimerization of Ebola GPΔmucin on protein nanoparticle vaccines has minimal effect on elicitation of neutralizing antibodies (PDF) (Front. Immunol.)
Abigail E. Powell, Duo Xu, Gillie A. Roth, Kaiming Zhang, Wah Chiu, Eric A. Appel, Peter S. Kim. Frontiers in Immunology (2022). 10.3389.
132. Simplified Purification of Glycoprotein-Modified Ferritin Nanoparticles for Vaccine Development (PDF) (ACS Biochem.)
Payton A.-B. Weidenbacher, Sriharshita Musunuri, Abigail E. Powell, Shaogeng Tang, Jonathan Do, Mrinmoy Sanyal, Peter S. Kim. Biochemistry (2022) 10.1021.
131. Chemically Modified Bacterial Sacculi as a Vaccine Microparticle Scaffold (PDF) (ACS Chem. Bio.)
Payton A.-B. Weidenbacher, Frances P. Rodriguez-Rivera, Mrinmoy Sanyal, Joshua A. Visser, Jonathan Do, Carolyn R. Bertozzi, Peter S. Kim. ACS Chemical Biology (2022) 10.1021.
130. Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins (PDF) (Cell Systems)
Brian L. Hie, Kevin K. Yang, Peter S. Kim. Cell Systems. (2022) 13, 1–12.
2021
129. Hydrogel-Based Slow Release of a Receptor-Binding Domain Subunit Vaccine Elicits Neutralizing Antibody Responses Against SARS-CoV-2 (PDF) (Adv. Mat.)
Emily C Gale, Abigail E Powell, Gillie A Roth, Emily L Meany, Jerry Yan, Ben S Ou, Abigail K Grosskopf, Julia Adamska, Vittoria C T M Picece, Andrea I d'Aquino, Bali Pulendran, Peter S Kim, Eric A Appel. Advanced Materials (2021) (Deerfield Beach, Fla.), 33(51), e2104362. doi.org/10.1002/adma.202104362.
128. A derivative of the D5 monoclonal antibody that targets the gp41 N-heptad repeat of HIV-1 with broad tier-2 neutralizing activity (PDF) (J Virol.)
Adonis A. Rubio, Maria V. Filsinger Interrante, Benjamin N. Bell, Clayton L. Brown, Theodora U.J. Bruun, Celia C. LaBranche, David C. Montefiori, Peter S. Kim. J Virol. (2021) 95(15):e0235020.
127. Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a naïve human antibody library (PDF) (Pro. Sci.)
Benjamin Nikola Bell, Abigail E. Powell, Carlos Rodriguez, Jennifer R Cochran, Peter S. Kim. Protein Science. (2021). 30: 716–727.
126. A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. (PDF) (ACS Cent. Sci.)
Abigail E. Powell, Kaiming Zhang, Mrinmoy Sanyal, Shaogeng Tang, Payton A. Weidenbacher, Shanshan Li, Tho D. Pham, John E. Pak, Wah Chiu, Peter S. Kim. ACS Cent. Sci. (2021).
125. The high-affinity immunoglobulin receptor FcγRI potentiates HIV-1 neutralization via antibodies against the gp41 N-heptad repeat.
(PDF) (PNAS)
David C. Montefiori, Maria V. Filsinger Interrante, Benjamin N. Bell, Adonis A. Rubio, Joseph G. Joyce, John W. Shiver, Celia C. LaBranche, and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2021).
124. Modeling human adaptive immune responses with tonsil organoids. (PDF) (Nat. Med.)
Lisa E. Wagar, Ameen Salahudeen, Christian M. Constantz, Ben S. Wendel, Michael M. Lyons, Vamsee Mallajosyula, Lauren P. Jatt, Julia Z. Adamska, Lisa K. Blum, Neha Gupta, Katherine J. L. Jackson, Fan Yang, Katharina Röltgen, Krishna M. Roskin, Kelly M. Blaine, Kara D. Meister, Iram N. Ahmad, Mario Cortese, Emery G. Dora, Sean N. Tucker, Anne I. Sperling, Aarti Jain, D. Huw Davies, Philip L. Felgner, Gregory B. Hammer, Peter S. Kim, William H. Robinson, Scott D. Boyd, Calvin J. Kuo, and Mark M. Davis. Nature Medicine (2021). 27: 125-135.
2020
123. Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome.
(PDF) (Sci. Immunol.)
Katharina Roltgen, Abigail E. Powell, Oliver F. Wirz, Bryan A. Stevens, Catherine A. Hogan, Javaria Najeeb, Molly Hunter, Hannah Wang, Malaya K. Sahoo, ChunHong Huang, Fumiko Yamamoto, Monali Manohar, Justin Manalac, Ana R. Ortelo-Cardoso, Tho D. Pham, Arjun Rustagi, Angela J. Rogers, Nigam H. Shah, Catherine A. Blish, Jennifer R. Cochran, Theodore S. Jardetzky, James L. Zehnder, Taia T. Wang, Balasubramanian Narasimhan, Saurabh Gombar, Robert Tibshirani, Kari C. Nadeau, Peter S. Kim, Benjamin A. Pinsky, and Scott D. Boyd. Science Immunology (2020). 5(24): eabe0240.
122. Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. (PDF) (Cell Host & Micr.)
Sandra C.A. Nielsen, Fan Yang, Katherine J.L. Jackson, Ramona A. Hoh, Katharina Roltgen, Grace H. Jean, Bryan A. Stevens, Ji-Yeun Lee, Arjun Rustagi, Angela J. Rogers, Abigail E. Powell, Molly Hunger, Javaria Najeeb, Ana R. Otrelo-Cardoso, Kathryn E. Yost, Bence Daniel, Kari C. Nadeau, Howard Y. Chang, Ansuman T. Satpathy, Theodore S. Jardetzky, Peter S. Kim, Taia T. Wang, Benjamin A. Pinsky, Catherine A. Blish, and Scott D. Boyd. Cell Host & Microbe (2020). 4: 516-525.e5.
121. Enhancing natural killer cell function with gp41-targeting bispecific antibodies to combat HIV infection, (PDF) (AIDS)
Nitya S. Ramadoss, Nancy Q. Zhao, Barbra A. Richardson, Philip M. Grant, Peter S. Kim, and Catherine A. Blish AIDS (2020). 34(9): 1313-1323.
120. Adaption of a conventional ELISA to a 96-well ELISA-Array for measuring the antibody responses to influenza virus proteins and vaccines.
(PDF) (J. Immunol. Methods)
Eric Waltari, Esteban Carabajal, Mrinmoy Sanyal, Natalia Friedland and Krista M. McCutcheon Journal of Immunological Methods (2020). 112789.
2019
119. A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery. (PDF)
Shaogeng Tang, and Peter S. Kim Proc. Natl. Acad. Sci. USA (2019). 116: 24500-24506.
118. Functional Enrichment and Analysis of Antigen-Specific Memory B Cell Antibody Repertoires in PBMCs. (PDF)
Eric Waltari, Aaron McGreever, Peter S. Kim and Krista M. McCutcheon Frontiers in Immunology (2019) 10: 1452.
117. FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences. (PDF)
Jenai Quan, Charles Langelier, Alison Kuchta, Joshua Batson, Noam Teyssier, Amy Lyden, Saharai Caldera, Aaron McGeever, Boris Dimitrov, Ryan King, Jordan Wilheim, Maxwell Murphy, Lara Pesce Ares, Katherine A. Travisano, Rene Sit, Roberto Amato, Davis R. Mumbengegwi, Jennifer L. Smith, Adam Bennett, Roly Gosling, Peter M. Mourani, Carolyn S. Calfee, Norma F. Neff, Eric D. Chow, Peter S. Kim, Bryan Greenhouse, Joseph L. DeRisi and Emily D. Crawford Nucleic Acids Research (2019) gkz418.
116. Protect, Modify, Deprotect (PMD): A strategy for creating vaccines to elicit antibodies targeting a specific epitope. (PDF)
Payton A. Weidenbacher and Peter S. Kim Proc. Natl. Acad. Sci. USA (2019) 116: 9947-9952.
115. Identification of HIV gp41-specific antibodies that mediate killing of infected cells. (PDF)
Katherine L. Williams, Megan Stumpf, Nicole Elise Naiman, Shilei Ding, Meghan Garrett, Theodore Gobillot, Dani Vezina, Katharine Dusenbury, Nitya S. Ramadoss, Ryan Basom, Peter S. Kim and Julie Overbaugh PLoS Pathog. (2019) 15(2): e1007572.
2018 AND EARLIER
114. Vaccination with peptide mimetics of the gp41 prehairpin fusion intermediate yields neutralizing antisera against HIV-1 isolates. (PDF)
Elisabetta Bianchi, Joseph G. Joyce, Michael D. Miller, Adam C. Finnefrock, Xiaoping Liang, Marco Finotto, Paolo Ingallinella, Philip McKenna, Michael Citron, Elizabeth Ottinger, Robert W. Hepler, Renee Hrin, Deborah Nahas, Chengwei Wu, David Montefiori, John W. Shiver, Antonella Pessi, and Peter S. Kim Proc. Natl. Acad. Sci. USA (2010) 107: 10655-10660.
113. A human monoclonal antibody neutralizes diverse HIV-1 isolates by binding a critical gp41 epitope. (PDF)
Michael D. Miller, Romas Geleziunas, Elisabetta Bianchi, Simon Lennard, Renee Hrin, Hangchun Zhang, Meiqing Lu, Zhiqiang An, Paolo Ingallinella, Marco Finotto, Marco Mattu, Adam C. Finnefrock, David Bramhill, James Cook, Debra M. Eckert, Richard Hampton, Mayuri Patel, Stephen Jarantow, Joseph Joyce, Gennaro Ciliberto, Ricarrdo Cortese, Ping Lu, William Strohl, William Schleif, Michael McElhaugh, Steven Lane, Christopher Lloyd, David Lowe, Jane Osbourn, Tristan Vaughan, Emilio Emini, Gaetano Barbato, Peter S. Kim, Daria J. Hazuda, John W. Shiver, and Antonello Pessi. Proc. Natl. Acad. Sci. USA (2005) 102: 14759-14764.
112. Structural Test of the Parameterized-backbone Method for Protein Design. (PDF)
Joseph J. Plecs, Pehr B. Harbury, Peter S. Kim and Tom Alber. J. Mol. Biol. (2004) 342: 289-297.
111. Protein Grafting of a HIV-1 Inhibiting Epitope. (PDF)
Samuel K. Sia and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2003) 100: 9756-9761.
110. Structure of the Bcr-Abl Oncoprotein Oligomerization Domain. (PDF)
Xun Zhao, Saghi Ghaffari, Harvey Lodish, Vladimir N. Malashkevich and Peter S. Kim. Nat. Struct. Biol. (2002) 9: 117-120.
109. Short Constrained Peptides that Inhibit HIV-1 Entry. (PDF)
Samuel K. Sia, Peter A. Carr, Andrea G. Cochran, Vladimir N. Malashkevich and Peter S. Kim. Proc. Natl. Acad. Sci. USA(2002) 99: 14664-14669.
108. Toward Development of a Screen to Identify Randomly Encoded, Foldable Sequences. (PDF)
Yoshihisa Hagihara and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2002) 99: 6619-6624.
107. TRIOLOGY: Discovery of Sequence-Structure Patterns Across Diverse Proteins. (PDF)
Philip Bradley, Peter S. Kim, and Bonnie Berger. Proc. Natl. Acad. Sci. USA (2002) 99: 8500-8505.
R&C #15. Mechanisms of Viral Membrane Fusion and Its Inhibition. (PDF)
Debra M. Eckert and Peter S. Kim. Annu. Rev. Biochem. (2001) 70: 777-810.
106. Design of Potent Inhibitors of HIV-1 Entry from the gp41 N-peptide Region. (PDF)
Debra M. Eckert and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2001) 98: 11187-11192.
105. Efficient Assembly of an HIV-1/MLV Gag-Chimeric Virus in Murine Cells. (PDF)
Benjamin K. Chen, Itay Rousso, Sung Shim and Peter S. Kim. Proc. Natl. Acad. Sci. (2001) 98: 15239-15244.
104. A Designed Protein with Packing Between Left-Handed and Right-Handed Helices. (PDF)
Samuel K. Sia and Peter S. Kim. Biochemistry (2001) 40: 8981-8989.
103. The Trimer-of-Hairpins Motif in Membrane Fusion: Visna Virus. (PDF)
Vladimir N. Malashkevich, Mona Singh and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2001) 98: 8502-8506.
102. Towards Predicting Coiled-Coil Protein Interactions. (PDF)
Mona Singh and Peter S. Kim. Proc. 5th Ann. Int. Conf. Comp. Mol. Biol. (2001) 279-286.
101. Protein Design of an HIV-1 Entry Inhibitor. (PDF)
Michael J. Root, Michael S. Kay and Peter S. Kim. Science (2001) 291: 884-888.
100. Side-chain Repacking Calculations for Predicting Structures and Stabilities of Heterodimeric Coiled Coils. (PDF)
Amy E. Keating, Vladimir N. Malashkevich, Bruce Tidor, and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2001) 98: 14825-14830.
99. Buried Polar Residues in Coiled-Coil Interfaces. (PDF)
David L. Akey, Vladimir N. Malashkevich and Peter S. Kim. Biochemistry (2001) 40: 6352-6360.
98. Structural Characterization of the Human Respiratory Syncytial Virus Fusion Protein Core. (PDF)
Xun Zhao, Mona Singh, Vladimir N. Malashkevich and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2000) 97: 14172-14177.
97. Palmitoylation of the HIV-1 Envelope Glycoprotein is Critical for Viral Infectivity. (PDF)
Itay Rousso, Mark B. Mixon, Benjamin K. Chen and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2000) 97: 13523-13525.
96. A Computationally Directed Screen Identifying Interacting Coiled Coils from Saccharomyces cerevisiae. (PDF)
John R. S. Newman, Ethan Wolf and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2000) 97: 13203-13208.
95. Folding of Bovine Pancreatic Trypsin Inhibitor (BPTI) Variants in Which Almost Half the Residues are Alanine. (PDF)
Yutaka Kuroda and Peter S. Kim. J. Mol. Biol. (2000) 298: 493-501.
94. Combinatorial Codons: A Computer Program to Approximate Amino Acid Probabilities with Biased Nucleotide Usage. (PDF)
Ethan Wolf and Peter S. Kim. Protein Science (1999) 8: 680-688.
93. LearnCoil-VMF: Computational Evidence for Coiled Coil-like Motifs in Many Viral Membrane-fusion Proteins. (PDF)
Mona Singh, Bonnie Berger and Peter S. Kim. J. Mol. Biol. (1999)290: 1031-1041.
92. a-Lactalbumin Forms a Compact Molten Globule in the Absence of Disulphide Bonds. (PDF)
Christina Redfield, Brenda A. Schulman, Michael A. Milhollen, Peter S. Kim and Christopher M. Dobson. Nat. Struct. Biol.(1999) 6: 948-952.
91. Core Structure of the Envelope Glycoprotein GP2 from Ebola Virus at 1.9 Å Resolution. (PDF)
Vladimir N. Malashkevich, Brian J. Schneider, Margaret L. McNally, Michael A. Milhollen, James X. Pang and Peter S. Kim. Proc. Natl. Acad. Sci. USA (1999) 96: 2662-2667.
90. Inhibiting HIV-1 Entry: Discovery of D-Peptide Inhibitors that Target the gp41 Coiled-Coil Pocket. (PDF)
Debra M. Eckert, Vladimir N. Malashkevich, Lily H. Hong, Peter A. Carr and Peter S. Kim. Cell (1999) 99: 103-115.
R&C #14. Interaction, Assembly and Processing at the Chemistry-Biology Interface. (PDF)
Alanna Schepartz and Peter S. Kim. Current Opinion Chem. Biol. (1998) 2: 9-10.
R&C #13. HIV Entry and Its Inhibition. (PDF)
David C. Chan and Peter S. Kim. Cell (1998) 93: 681-684.
89. A Specific Hydrophobic Core in the a-Lactalbumin Molten Globule. (PDF)
Lawren C. Wu and Peter S. Kim J. Mol. Biol. (1998) 280: 175-182.
88. Computational Learning Reveals Coiled Coil-Like Motifs in Histidine Kinase Linker Domains. (PDF)
Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger and Andrea G. Cochran. Proc. Natl. Acad. Sci. USA (1998) 95: 2738-2743.
87. A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil. (PDF)
Martha G. Oakley and Peter S. Kim Biochemistry (1998) 37: 12603-12610.
86. Crystal Structure of the Simian Immunodeficiency Virus (SIV) gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of gp41 Peptides. (PDF)
Vladimir N. Malashkevich, David C. Chan, Christine T. Chutkowski and Peter S. Kim. Proc. Natl. Acad. Sci. USA (1998) 95: 9134-9139.
85. High-Resolution Protein Design with Backbone Freedom. (PDF)
Pehr B. Harbury, Joseph J. Plecs, Bruce Tidor, Tom Alber and Peter S. Kim Science (1998) 282: 1462-1467.
84. Crystal Structure of GCN4-pIQI, a Trimeric Coiled Coil With Buried Polar Residues. (PDF)
Debra M. Eckert, Vladimir N. Malashkevich and Peter S. Kim J. Mol. Biol. (1998) 284: 859-865.
83. Evidence that a Prominent Cavity in the Coiled Coil of HIV type 1 gp41 is an Attractive Drug Target. (PDF)
David C. Chan, Christine T. Chutkowski and Peter S. Kim Proc. Natl. Acad. Sci. USA (1998) 95: 15613-15617.
R&C #12. A Trimeric Structural Subdomain of the HIV-1 Transmembrane Glycoprotein. (PDF)
Min Lu and Peter S. Kim J. Biomol. Struct. and Dyn. (1997) 15: 465-471.
R&C #11. Core Structure of gp41 from the HIV Envelope Glycoprotein and Implications for Membrane Fusion.
David C. Chan and Peter S. Kim Onzième Colloque Des Cent Gardes (1997) (M. Girard & B. Dodet eds.) Elsevier Press, 105-111.
82. Hydrophobic Sequence Minimization of the a-Lactalbumin Molten Globule. (PDF)
Lawren C. Wu and Peter S. Kim Proc. Natl. Acad. Sci. USA (1997) 94: 14314-14319.
81. MultiCoil: A Program for Predicting Two- and Three-Stranded Coiled Coils. (PDF)
Ethan Wolf, Peter S. Kim and Bonnie Berger Protein Science (1997) 6: 1179-1189.
80. Bioactive and Nuclease-Resistant L-DNA Ligand of Vasopressin. (PDF)
Kelly P. Williams, Xiao-Hong Liu, Ton N.M. Schumacher, Herbert Y. Lin, Dennis A. Ausiello, Peter S. Kim and David P. Bartel Proc. Natl. Acad. Sci. USA(1997) 94: 11285-11290.
79. A Residue-Specific NMR View of the Non-Cooperative Unfolding of a Molten Globule. (PDF)
Brenda A. Schulman, Peter S. Kim, Christopher M. Dobson and Christina Redfield Nat. Struct. Biol. (1997) 4: 630-634.
78. Protein Dissection of the Antiparallel Coiled Coil from Escherichia coli Seryl tRNA Synthetase. (PDF)
Martha G. Oakley and Peter S. Kim Biochemistry (1997) 36: 2544-2549.
77. NMR Structure of the 35-Residue Villin Headpiece Subdomain.
C. James McKnight, Paul T. Matsudaira and Peter S. Kim Nat. Struct. Biol. (1997) 4: 180-184.
76. Structure of a Murine Leukemia Virus Receptor-Binding Glycoprotein at 2.0 Angstrom Resolution. (PDF)
Deborah Fass, Robert A. Davey, Christian A. Hamson, Peter S. Kim, James M. Cunningham and James M. Berger Science(1997) 277: 1662-1666.
75. Molecular Basis of Familial Hypercholesterolaemia from Structure of LDL Receptor Module. (PDF)
Deborah Fass, Stephen Blacklow, Peter S. Kim and James M. Berger Nature (1997) 388: 691-693.
74. Core Structure of gp41 from the HIV Envelope Glycoprotein. (PDF)
David C. Chan, Deborah Fass, James M. Berger and Peter S. Kim Cell (1997) 89: 263-273.
73. Influenza Hemagglutinin is Spring-Loaded by a Metastable Native Conformation. (PDF)
Chavela M. Carr, Charu Chaudhry and Peter S. Kim Proc. Natl. Acad. Sci. USA (1997) 94: 14306-14313.
72. Disulfide Determinants of Calcium-Induced Packing in a-Lactalbumin. (PDF)
Lawren C. Wu, Brenda A. Schulman, Zheng-yu Peng and Peter S. Kim Biochemistry (1996) 35: 859-863.
71. Identification of D-Peptide Ligands through Mirror-Image Phage Display. (PDF)
Ton N.M. Schumacher, Lorenz M. Mayr, Daniel L. Minor, Jr., Michael A. Milhollen, Michael W. Burgess and Peter S. Kim Science (1996) 271: 1854-1857.
70. Proline Scanning Mutagenesis of a Molten Globule Reveals Non-Cooperative Formation of a Protein’s Overall Topology. (PDF)
Brenda A. Schulman and Peter S. Kim Nature Structural Biology (1996) 3: 682-687.
69. Context-Dependent Secondary Structure Formation of a Designed Protein Sequence. (PDF)
Daniel L. Minor, Jr. and Peter S. Kim Nature (1996) 380: 730-734.
68. A Thermostable 35-Residue Subdomain within Villin Headpiece. (PDF)
C. James McKnight, Don S. Doering, Paul T. Matsudaira and Peter S. Kim J. Mol. Biol. (1996) 260: 126-134.
67. Interhelical Salt Bridges, Coiled-Coil Stability, and Specificity of Dimerization: Response. (PDF)
Kevin J. Lumb and Peter S. Kim Science (1996) 271: 1136-1138.
66. Retrovirus Envelope Domain at 1.7 Å Resolution. (PDF)
Deborah Fass, Stephen C. Harrison and Peter S. Kim Nat. Struct. Biol. (1996) 3: 465-469.
65. Rapid Formation of the Native 14-38 Disulfide Bond in the Early Stages of BPTI Folding. (PDF)
Michal Dadlez and Peter S. Kim Biochemistry (1996) 35: 16153-16164.
64. Imitation of Escherichia coli Aspartate Receptor Signaling in Engineered Dimers of the Cytoplasmic Domain. (PDF)
Andrea G. Cochran and Peter S. Kim Science (1996) 271: 1113-1116.
63. Protein Folding and Calcium Binding Defects Arising from Familial Hypercholesterolemia Mutations of the LDL Receptor. (PDF)
Stephen C. Blacklow and Peter S. Kim Nat. Struct. Biol. (1996) 3: 758-762.
62. Contribution of Individual Side-Chains to the Stability of BPTI Examined by Alanine-Scanning Mutagenesis. (PDF)
Myeong-Hee Yu, Jonathan S. Weissman and Peter S. Kim J. Mol. Biol. (1995) 249: 388-397.
61. Bipartite Structure of the a-Lactalbumin Molten Globule. (PDF)
Lawren C. Wu, Zheng-yu Peng and Peter S. Kim. Nat. Struct. Biol. (1995) 2: 281-286.
60. A Kinetic Explanation for the Rearrangement Pathway of BPTI Folding. (PDF)
Jonathan S. Weissman and Peter S. Kim. Nat. Struct. Biol. (1995) 2: 1123-1130.
59. Different Subdomains are Most Protected from Hydrogen Exchange in the Molten Globule and Native States of Human a-Lactalbumin. (PDF)
Brenda A. Schulman, Christina Redfield, Zheng-yu Peng, Christopher M. Dobson and Peter S. Kim J. Mol. Biol. (1995) 253: 651-657.
58. Local Structural Preferences in the a-Lactalbumin Molten Globule. (PDF)
Zheng-yu Peng, Lawren C. Wu and Peter S. Kim Biochemistry (1995) 34: 3248-3252.
57. Does the Molten Globule Have a Native-Like Tertiary Fold? (PDF)
Zheng-yu Peng, Lawren C. Wu, Brenda A. Schulman and Peter S. Kim Phil. Trans. Royal Soc. B, (1995) 348: 43-47.
56. A Buried Polar Interaction Imparts Structural Uniqueness in a Designed Heterodimeric Coiled Coil. (PDF)
Kevin J. Lumb and Peter S. Kim Biochemistry (1995) 34: 8642-8648.
55. Measurement of Interhelical Electrostatic Interactions in the GCN4 Leucine Zipper. (PDF)
Kevin J. Lumb and Peter S. Kim Science (1995) 268: 436-439.
54. A Trimeric Structural Domain of the HIV-1 Transmembrane Glycoprotein. (PDF)
Min Lu, Stephen C. Blacklow and Peter S. Kim Nat. Struct. Biol. (1995) 2: 1075-1082.
53. Repacking Protein Cores with Backbone Freedom: Structure Prediction for Coiled Coils. (PDF)
Pehr B. Harbury, Bruce Tidor and Peter S. Kim Proc. Natl. Acad. Sci. USA (1995) 92: 8408-8412.
52. Dissection of a Retrovirus Envelope Protein Reveals Structural Similarity to Influenza Hemagglutinin. (PDF)
Deborah Fass and Peter S. Kim Current Biology (1995) 5: 1377-1383.
51. A Third Native One-Disulfide Intermediate in the Folding of Bovine Pancreatic Trypsin Inhibitor.
Michal Dadlez and Peter S. Kim Nat. Struct. Biol. (1995) 2: 674-679.
50. Intermediates in the Folding of the Membrane Protein Bacteriorhodopsin. (PDF)
Paula J. Booth, Sabine L. Flitsch, Lawrence J. Stern, Duncan A. Greenhalgh, Peter S. Kim and H. Gobind Khorana Nat. Struct. Biol. (1995) 2: 139-143.
49. A Trimeric Subdomain of the Simian Immunodeficiency Virus Envelope Glycoprotein. (PDF)
Stephen C. Blacklow, Min Lu and Peter S. Kim Biochemistry (1995) 34: 14955-14962.
48. Predicting Coiled Coils by Use of Pairwise Residue Correlations. (PDF)
Bonnie Berger, David B. Wilson, Ethan Wolf, Theodore Tonchev, Maria Milla and Peter S. Kim Proc. Natl. Acad. Sci. USA(1995) 92: 8259-8263.
R&C #10. Flu Virus Invasion: Halfway There. (PDF)
Chavela M. Carr and Peter S. Kim Science (1994) 265: 234-236.
47. Formation of a Native-Like Subdomain in a Partially Folded Intermediate of Bovine Pancreatic Trypsin Inhibitor. (PDF)
Jonathan P. Staley and Peter S. Kim Protein Science (1994) 3: 1822-1832.
46. Hydrogen Exchange in BPTI Variants that Do Not Share a Common Disulfide Bond. (PDF)
Brenda A. Schulman and Peter S. Kim Protein Science (1994) 3: 2226-2232.
45. A Protein Dissection Study of a Molten Globule. (PDF)
Zheng-yu Peng and Peter S. Kim Biochemistry (1994) 33: 2136-2141.
44. Context is a Major Determinant of β-Sheet Propensity. (PDF)
Daniel L. Minor, Jr. and Peter S. Kim Nature (1994) 371: 264-267.
43. Measurement of the β-sheet-forming propensities of amino acids. (PDF)
Daniel L. Minor, Jr. and Peter S. Kim Nature (1994) 371: 264-267.
42. Subdomain Folding of the Coiled Coil Leucine Zipper from the bZIP Transcriptional Activator GCN4. (PDF)
Kevin J. Lumb, Chavela M. Carr and Peter S. Kim Biochemistry (1994)33: 7361-7367.
41. Formation of a Hydrophobic Cluster in Denatured Bovine Pancreatic Trypsin Inhibitor. (PDF)
Kevin J. Lumb and Peter S. Kim J. Mol. Biol. (1994) 236: 412-420.
40. Crystal Structure of an Isoleucine-Zipper Trimer. (PDF)
Pehr B. Harbury, Peter S. Kim and Tom Alber Nature (1994) 371: 80-83.
39. Efficient Catalysis of Disulphide Bond Rearrangements by Protein Disulphide Isomerase. (PDF)
Jonathan S. Weissman and Peter S. Kim Nature (1993) 365: 185-188.
38. Peptide ‘Velcro’: Design of a Heterodimeric Coiled Coil. (PDF)
Erin K. O’Shea, Kevin J. Lumb and Peter S. Kim Current Biology (1993) 3: 658-667.
37. Electrostatic Screening of Charge and Dipole Interactions with the Helix Backbone. (PDF)
David J. Lockhart and Peter S. Kim Science (1993) 260: 198-202.
36. A Switch Between Two-, Three-, and Four-Stranded Coiled Coils in GCN4 Leucine Zipper Mutants. (PDF)
Pehr B. Harbury, Tao Zhang, Peter S. Kim and Tom Alber Science (1993) 262: 1401-1407.
35. A Spring-Loaded Mechanism for the Conformational Change of Influenza Hemagglutinin. (PDF)
Chavela M. Carr and Peter S. Kim Cell (1993) 73: 823-832.
34. The Pro Region of BPTI Facilitates Folding. (PDF)
Jonathan S. Weissman and Peter S. Kim Cell (1992) 71: 841-851.
33. Kinetic Role of Nonnative Species in the Folding of Bovine Pancreatic Trypsin Inhibitor. (PDF)
Jonathan S. Weissman and Peter S. Kim Proc. Natl. Acad. Sci. USA (1992) 89: 9900-9904.
32. The Disulfide Folding Pathway of BPTI: Response.
Jonathan S. Weissman and Peter S. Kim Science (1992) 256: 111-114.
31. Minimum Length of a Sequence-Specific DNA Binding Peptide. (PDF)
Robert V. Talanian, C. James McKnight, Rheba Rutkowski and Peter S. Kim Biochemistry (1992) 31: 6871-6875.
30. Complete Folding of Bovine Pancreatic Trypsin Inhibitor with Only a Single Disulfide Bond. (PDF)
Jonathan P. Staley and Peter S. Kim Proc. Natl. Acad. Sci. USA(1992) 89: 1519-1523.
29. Mechanism of Specificity in the Fos-Jun Oncoprotein Heterodimer. (PDF)
Erin K. O'Shea, Rheba Rutkowski and Peter S. Kim Cell (1992) 68: 699-708.
28. Internal Stark Effect Measurement of the Electric Field at the Amino Terminus of an a-Helix. (PDF)
David J. Lockhart and Peter S. Kim Science (1992) 257: 947-951.
R&C #9. Modular Structure of Transcription Factors: Implications for Gene Regulation. (PDF)
Alan D. Frankel and Peter S. Kim Cell (1991) 65: 717-719.
R&C #8. Folding and Binding: Editorial Overview. (PDF)
Thomas E. Creighton and Peter S. Kim Current Opinion Struct. Biol.(1991) 1: 3-4.
27. Reexamination of the Folding of BPTI: Predominance of Native Intermediates. (PDF)
Jonathan S. Weissman and Peter S. Kim Science (1991) 253: 1386-1393.
26. X-ray Scattering Indicates that the Leucine Zipper is a Coiled Coil. (PDF)
Randy Rasmussen, Dominic Benvegnu, Erin K. O'Shea, Peter S. Kim and Tom Alber Proc. Natl. Acad. Sci. USA (1991) 88: 561-564.
25. X-ray Structure of the GCN4 Leucine Zipper, a Two-Stranded, Parallel Coiled Coil. (PDF)
Erin K. O'Shea, Juli D. Klemm, Peter S. Kim and Tom Alber Science (1991) 254: 539-544.
24. Evaluating the Effects of a Single Amino Acid Substitution on Both the Native and Denatured States of a Protein. (PDF)
Tiao-Yin Lin and Peter S. Kim Proc. Natl. Acad. Sci. USA (1991) 88: 10573-10577.
23. Periodicity of Amide Proton Exchange Rates in a Coiled-Coil Leucine Zipper Peptide. (PDF)
Elizabeth M. Goodman and Peter S. Kim Biochemistry (1991) 30: 11615-11620.
R&C #7. A Protein Folding Intermediate Analogue: Design, Synthesis, and Characterization.
Terrence G. Oas and Peter S. Kim Protein Folding (1990) (L.M. Gierasch & S.J. King eds.) AAAS Press, 123-128.
R&C #6. Intermediates in the Folding Reactions of Small Proteins. (PDF)
Peter S. Kim and Robert L. Baldwin Annu. Rev. Biochem. (1990) 59: 631-660.
22. Sequence-Specific DNA Binding by a Short Peptide Dimer. (PDF)
Robert V. Talanian, C. James McKnight and Peter S. Kim Science (1990) 249: 769-771.
21. Role of a Subdomain in the Folding of Bovine Pancreatic Trypsin Inhibitor. (PDF)
Jonathan P. Staley and Peter S. Kim Nature (1990) 344: 685-688.
20. Secondary Structure of a Leucine Zipper Determined by Nuclear Magnetic Resonance Spectroscopy. (PDF)
Terrence G. Oas, Lawrence P. McIntosh, Erin K. O'Shea, Frederick W. Dahlquist and Peter S. Kim Biochemistry (1990) 29: 2891-2894.
19. Sequence Requirements for Coiled-Coils: Analysis with l Repressor-GCN4 Leucine Zipper Fusions. (PDF)
James C. Hu, Erin K. O'Shea, Peter S. Kim and Robert T. Sauer Science (1990) 250: 1400-1403.
18. Tests of Isolated b-Sheet Formation in a Cyclic Peptide from BPTI.
Elizabeth M. Goodman and Peter S. Kim Current Research in Protein Chemistry (1990) (J.J. Villafranca, ed.) Academic Press, 301-308.
17. Preferential Heterodimer Formation by Isolated Leucine Zippers from Fos and Jun. (PDF)
Erin K. O'Shea, Rheba Rutkowski, Walter F. Stafford III and Peter S. Kim Science (1989) 245: 646-648.
16. Evidence that the Leucine Zipper is a Coiled Coil. (PDF)
Erin K. O'Shea, Rheba Rutkowski and Peter S. Kim Science (1989) 243: 538-542.
15. Urea Dependence of Thiol-Disulfide Equilibria in Thioredoxin: Confirmation of the Linkage Relationship and a Sensitive Assay for Structure. (PDF)
Tiao-Yin Lin and Peter S. Kim Biochemistry (1989) 28: 5282-5287.
14. Folding of a Peptide Corresponding to the a-Helix in Bovine Pancreatic Trypsin Inhibitor. (PDF)
Elizabeth M. Goodman and Peter S. Kim Biochemistry (1989) 28: 4343-4347.
R&C #5. Passing the First Milestone in Protein Design. (PDF)
Peter S. Kim Protein Eng. (1988) 2: 249-250.
13. A Peptide Model of a Protein Folding Intermediate. (PDF)
Terrence G. Oas and Peter S. Kim Nature (1988) 336: 42-48.
12. Strategy for Obtaining Non-Native Protein Structures Using Antibody Cross-Reactions. (PDF)
Peter S. Kim Biophys. Chem.(1988) 31: 107-111.
R&C #4. The C-Peptide Helix from Ribonuclease A Considered as an Autonomous Folding Unit. (PDF)
Kevin R. Shoemaker, Robert Fairman, Peter S. Kim, Eunice J. York, John M. Stewart and Robert L. Baldwin Cold Spring Harb. Symp. Quant. Biol. (1987) 52: 391-398.
11. Tests of the Helix Dipole Model for Stabilization of a-Helices. (PDF)
Kevin R. Shoemaker, Peter S. Kim, Eunice J. York, John M. Stewart and Robert L. Baldwin Nature (1987) 326: 563-567.
R&C #3. Amide Proton Exchange as a Probe of Protein Folding Pathways. (PDF)
Peter S. Kim Meth. Enzymology (1986) 131: 136-156.
10. Effects of Denaturants on Amide Proton Exchange Rates: A Test for Structure in Protein Fragments and Folding Intermediates. (PDF)
David Loftus, George O. Gbenle, Peter S. Kim and Robert L. Baldwin Biochemistry (1986) 25: 1428-1436.
9. Analysis of a Leprosy-Specific Antibody Epitope.
Wayne B. Brown, Wendy A. Larrabee and Peter S. Kim Lepr. Rev. (1986) 57: 157-162.
8. Nature of the Charged-Group Effect on the Stability of the C-Peptide Helix. (PDF)
Kevin R. Shoemaker, Peter S. Kim, David N. Brems, Susan Marqusee, Eunice J. York, Irwin M. Chaiken, John M. Stewart and Robert L. Baldwin Proc. Natl. Acad. Sci. USA (1985) 82: 2349-2353.
7. A Helix Stop Signal in the Isolated S-Peptide of Ribonuclease A. (PDF)
Peter S. Kim and Robert L. Baldwin Nature (1984) 307: 329-334.
R&C #2. Strategy for Trapping Intermediates in the Folding of Ribonuclease and for Using 1H-NMR to Determine Their Structures. (PDF)
Kunihiro Kuwajima, Peter S. Kim and Robert L. Baldwin Biopolymers(1983) 22: 59-67.
R&C #1. Specific Intermediates in the Folding Reactions of Small Proteins and the Mechanism of Protein Folding. (PDF)
Peter S. Kim and Robert L. Baldwin Annu. Rev. Biochem. (1982) 51: 459-489.
6. A Competing Salt-bridge Suppresses Helix Formation by the Isolated C-Peptide Carboxylate of Ribonuclease A. (PDF)
Peter S. Kim, Andrzej Bierzynski and Robert L. Baldwin J. Mol. Biol. (1982) 162: 187-199.
5. Influence of Charge on the Rate of Amide Proton Exchange. (PDF)
Peter S. Kim and Robert L. Baldwin Biochemistry (1982) 21: 1-5.
4. A Salt Bridge Stabilizes the Helix Formed by Isolated C-Peptide of RNase A. (PDF)
Andrzej Bierzynski, Peter S. Kim and Robert L. Baldwin Proc. Natl. Acad. Sci. USA (1982) 79: 2470-2474.
3. Acetylcholine Receptor-Controlled Ion Flux in Electroplax Membrane Vesicles: Identification and Characterization of Membrane Properties that Affect Ion Flux Measurements. (PDF)
Peter S. Kim and George P. Hess J. Membrane Biol. (1981) 58: 203-211.
2. Inactivation (Desensitization) of the Acetylcholine Receptor in Electrophorous electricus Membrane Vesicles by Carbamylcholine: Comparison Between Ion Flux and a-Bungarotoxin Binding. (PDF)
Nava Epstein, George P. Hess, Peter S. Kim and Richard L. Noble J. Membrane Biol. (1980) 56: 133-137.
1. Structural Intermediates Trapped During the Folding of Ribonuclease A by Amide Proton Exchange. (PDF)
Peter S. Kim and Robert L. Baldwin Biochemistry (1980) 19: 6124-6129.
published preprints
22. Payton A Weidenbacher, Natalia Friedland, Mrinmoy Sanyal, Mary Kate Morris, Jonathan Do, Carl Hanson, Peter S. Kim. bioRxiv (2023). Decreased efficacy of a COVID-19 vaccine due to mutations present in early SARS-CoV-2 variants of concern. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2023.06.27.546764v2
21. Duo Xu, Abigail E. Powell, Ashley Utz, Mrinmoy Sanyal, Jonathan Do, J.J. Patten, Juan I. Moliva, Nancy J. Sullivan, Robert A. Davey, Peter S. Kim. bioRxiv (2023). Design of universal Ebola virus vaccine candidates via immunofocusing. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2023.10.14.562364v1
20. Duo Xu, Chunfeng Li, Ashley Utz, Payton A.B. Weidenbacher, Shaogeng Tang, Mrinmoy Sanyal, Bali Pulendran, Peter S. Kim. bioRxiv (2022). Designing epitope-focused vaccines via antigen reorientation. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.12.20.521291v1
19. Ozan Kumru, Mrinmoy Sanyal, Natalia Friedland, John Hickey, Richa Joshi, Payton Weidenbacher, Jonathan Do, Ya-Chen Cheng, Peter S. Kim, Sangeeta B Joshi, David B Volkin. bioRxiv (2023). Formulation development and comparability studies with an aluminum-salt adjuvanted SARS-CoV-2 Spike ferritin nanoparticle vaccine antigen produced from two different cell lines. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2023.04.03.535447v1
18. Brian L Hie, Duo Xu, Varun R Shanker, Theodora UJ Bruun, Payton A Weidenbacher, Shaogeng Tang, Peter S Kim. bioRxiv (2022). Efficient evolution of human antibodies from general protein language models and sequence information alone. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.04.10.487811v1
17. Payton A.-B. Weidenbacher, Mrinmoy Sanyal, Natalia Friedland, Shaogeng Tang, Prabhu S. Arunachalam, Mengyun Hu, Ozan S. Kumru, Mary Kate Morris, Jane Fontenot, Lisa Shirreff, Jonathan Do, Ya-Chen Cheng, Gayathri Vasudevan, Mark B. Feinberg, Francois J. Villinger, Carl Hanson, Sangeeta B. Joshi, David B. Volkin, Bali Pulendran, Peter S. Kim. bioRxiv (2022). A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.12.25.521784v1
16. Theodora U. J. Bruun, Shaogeng Tang, Graham Erwin, Lindsay Deis, Daniel Fernandez, Peter S. Kim. bioRxiv (2022). Structure-guided stabilization improves the ability of the HIV-1 gp41 hydrophobic pocket to elicit neutralizing antibodies. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.12.22.521671v1
15. Benjamin N. Bell, Theodora U. J. Bruun, Natalia Friedland, Peter S. Kim. bioRxiv (2022). HIV-1 neutralization tiers are not relevant for inhibitors targeting the pre-hairpin intermediate. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.10.06.511062v1
14. Soohyun Kim, Maria V. Filsinger Interrante, Peter S. Kim. bioRxiv (2022). Enhancing HIV-1 neutralization by increasing the local concentration of MPER-directed bnAbs. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.10.23.513422v1
13. Shaogeng Tang, Yonggang Lu, Will M Skinner, Mrinmoy Sanyal, Polina V Lishko, Masahito Ikawa, Peter S. Kim. bioRxiv (2022). Human sperm TMEM95 binds eggs and facilitates membrane fusion (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.06.10.495573v1
12. Payton A.-B. Weidenbacher, Eric Waltari, Izumi de los Rios Kobara, Benjamin N. Bell, John E. Pak, Peter S. Kim. bioRxiv (2022). Converting non-neutralizing SARS-CoV-2 antibodies targeting conserved epitopes into broad-spectrum inhibitors through receptor blockade (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2022.01.24.477625v1
11. Brian L. Hie, Kevin K. Yang, Peter S. Kim. Cell Systems (2022). Evolutionary velocity with protein language models (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2021.06.07.447389v1
10. Benjamin Nikola Bell, Abigail E. Powell, Carlos Rodriguez, Jennifer R Cochran, Peter S. Kim. Protein Science. (2021). Neutralizing antibodies targeting the SARS-CoV-2 receptor binding domain isolated from a naïve human antibody library (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2021.01.07.425806v1
9. Abigail E. Powell, Kaiming Zhang, Mrinmoy Sanyal, Shaogeng Tang, Payton A. Weidenbacher, Shanshan Li, Tho D. Pham, John E. Pak, Wah Chiu, Peter S. Kim. ACS Cent. Sci. (2021). A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2020.08.28.272518v1
8. David C. Montefiori, Maria V. Filsinger Interrante, Benjamin N. Bell, Adonis A. Rubio, Joseph G. Joyce, John W. Shiver, Celia C. LaBranche, and Peter S. Kim. Proc. Natl. Acad. Sci. USA (2021). The high-affinity immunoglobulin receptor FcγRI potentiates HIV-1 neutralization via antibodies against the gp41 N-heptad repeat. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2020.08.27.271064v1
7. Daniel Brigger, Michael P. Horn, Luke F. Pennington, Abigail E. Powell, Vanja Piezzi, Lauro Damonti, Patricia Iseli, Christoph Hauser, Tanja K. Froehlich, Martin F. Bachmann, Stephen L. Leib, Pascal Bittel, Martin Fiedler, Carlo Largiader, Jonas Marschall, Hanspeter Stalder, Peter S. Kim, Theodore S. Jardetsky, Alexander Eggel, and Michael Nagler Allergy (2021). 76: 853-865, Accuracy of serological testing for SARS‐CoV‐2 antibodies: First results of a large mixed‐method evaluation study. (PDF)
Preprint: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3605126
6. Nielsen, S.C.A., Yang, F., Jackson, K.J.L., Hoh, R.A., Röltgen, K., Jean, G.H., Stevens, B.A., Lee, J.-Y., Rustagi, A., Rogers, A.J., Powell, A.E., Hunter, M., Najeeb, J., Otrelo-Cardoso, A.R., Yost, K.E., et al. Cell Host Microbe (2020) Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. Cell Host Microbe. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2020.07.08.194456v1
5. Nitya S. Ramadoss, Nancy Q. Zhao, Barbra A. Richardson, Philip M. Grant, Peter S. Kim, and Catherine A. Blish AIDS (2020). 34(9): 1313-1323. Enhancing natural killer cell function with gp41-targeting bispecific antibodies to combat HIV infection. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/760280v1
4. Eric Waltari, Esteban Carabajal, Mrinmoy Sanyal, Natalia Friedland and Krista M. McCutcheon Journal of Immunological Methods (2020). 112789. Adaption of a conventional ELISA to a 96-well ELISA-Array for measuring the antibody responses to influenza virus proteins and vaccines. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/2019.12.20.885285v2
3. Shaogeng Tang, and Peter S. Kim Proc. Natl. Acad. Sci. USA (2019). 116: 24500-24506. A high-affinity human PD-1/PD-L2 complex informs avenues for small-molecule immune checkpoint drug discovery. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/786319v1.full
2. Eric Waltari, Aaron McGreever, Peter S. Kim and Krista M. McCutcheon Frontiers in Immunology (2019) 10: 1452. Functional Enrichment and Analysis of Antigen-Specific Memory B Cell Antibody Repertoires in PBMCs. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/557769v1
1. Payton A. Weidenbacher and Peter S. Kim Proc. Natl. Acad. Sci. USA (2019) 116: 9947-9952. Protect, Modify, Deprotect (PMD): A strategy for creating vaccines to elicit antibodies targeting a specific epitope. (PDF)
Preprint: https://www.biorxiv.org/content/10.1101/507541v1