Original Research Articles

(see bottom of the page for Review Articles)

117. Eric Waltari, Aaron McGreever, Peter S. Kim and Krista M. McCutcheon bioRxiv (2019) 557769. Functional Enrichment and Analysis of Antigen-Specific Memory B Cell Antibody Repertoires in PBMCs. (LINK)

116. Payton A. Weidenbacher and Peter S. Kim bioRxiv (2018) 507541. Protect, Modify, Deprotect (PMD): A strategy for creating vaccines to elicit antibodies targeting a specific epitope. (LINK)

115. 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. Identification of HIV gp41-specific antibodies that mediate killing of infected cells. (LINK)

114. 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. Vaccination with peptide mimetics of the gp41 prehairpin fusion intermediate yields neutralizing antisera against HIV-1 isolates. (PDF)

113. 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. A human monoclonal antibody neutralizes diverse HIV-1 isolates by binding a critical gp41 epitope. (PDF)

112. Joseph J. Plecs, Pehr B. Harbury, Peter S. Kim and Tom Alber J. Mol. Biol. (2004) 342: 289-297. Structural Test of the Parameterized-backbone Method for Protein Design.

111. Samuel K. Sia and Peter S. Kim Proc. Natl. Acad. Sci. USA (2003) 100: 9756-9761. Protein Grafting of a HIV-1 Inhibiting Epitope. (PDF)

110. Xun Zhao, Saghi Ghaffari, Harvey Lodish, Vladimir N. Malashkevich and Peter S. Kim Nat. Struct. Biol. (2002) 9: 117-120. Structure of the Bcr-Abl Oncoprotein Oligomerization Domain. (PDF)

109. 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. Short Constrained Peptides that Inhibit HIV-1 Entry. (PDF)

108. Yoshihisa Hagihara and Peter S. Kim Proc. Natl. Acad. Sci. USA (2002) 99: 6619-6624. Toward Development of a Screen to Identify Randomly Encoded, Foldable Sequences. (PDF)

107. Philip Bradley, Peter S. Kim, and Bonnie Berger Proc. Natl. Acad. Sci. USA (2002) 99: 8500-8505. TRIOLOGY: Discovery of Sequence-Structure Patterns Across Diverse Proteins. (PDF)

106. Debra M. Eckert and Peter S. Kim Proc. Natl. Acad. Sci. USA (2001) 98: 11187-11192. Design of Potent Inhibitors of HIV-1 Entry from the gp41 N-peptide Region. (PDF)

105. Benjamin K. Chen, Itay Rousso, Sung Shim and Peter S. Kim Proc. Natl. Acad. Sci. (2001) 98: 15239-15244. Efficient Assembly of an HIV-1/MLV Gag-Chimeric Virus in Murine Cells. (PDF)

104. Samuel K. Sia and Peter S. Kim Biochemistry (2001) 40: 8981-8989. A Designed Protein with Packing Between Left-Handed and Right-Handed Helices. (PDF)

103. Vladimir N. Malashkevich, Mona Singh and Peter S. Kim Proc. Natl. Acad. Sci. USA (2001) 98: 8502-8506. The Trimer-of-Hairpins Motif in Membrane Fusion: Visna Virus. (PDF)

102. Mona Singh and Peter S. Kim Proc. 5th Ann. Int. Conf. Comp. Mol. Biol. (2001) 279-286. Towards Predicting Coiled-Coil Protein Interactions. (PDF)

101. Michael J. Root, Michael S. Kay and Peter S. Kim Science (2001) 291: 884-888. Protein Design of an HIV-1 Entry Inhibitor. (PDF)

100. Amy E. Keating, Vladimir N. Malashkevich, Bruce Tidor, and Peter S. Kim Proc. Natl. Acad. Sci. USA (2001) 98: 14825-14830. Side-chain Repacking Calculations for Predicting Structures and Stabilities of Heterodimeric Coiled Coils. (PDF)

99. David L. Akey, Vladimir N. Malashkevich and Peter S. Kim Biochemistry (2001) 40: 6352-6360. Buried Polar Residues in Coiled-Coil Interfaces. (PDF)

98. Xun Zhao, Mona Singh, Vladimir N. Malashkevich and Peter S. Kim Proc. Natl. Acad. Sci. USA (2000) 97: 14172-14177. Structural Characterization of the Human Respiratory Syncytial Virus Fusion Protein Core. (PDF)

97. Itay Rousso, Mark B. Mixon, Benjamin K. Chen and Peter S. Kim Proc. Natl. Acad. Sci. USA (2000) 97: 13523-13525. Palmitoylation of the HIV-1 Envelope Glycoprotein is Critical for Viral Infectivity. (PDF)

96. John R. S. Newman, Ethan Wolf and Peter S. Kim Proc. Natl. Acad. Sci. USA (2000) 97: 13203-13208. A Computationally Directed Screen Identifying Interacting Coiled Coils from Saccharomyces cerevisiae. (PDF)

95. Yutaka Kuroda and Peter S. Kim J. Mol. Biol. (2000) 298: 493-501. Folding of Bovine Pancreatic Trypsin Inhibitor (BPTI) Variants in Which Almost Half the Residues are Alanine. (PDF)

94. Ethan Wolf and Peter S. Kim Protein Science (1999) 8: 680-688. Combinatorial Codons: A Computer Program to Approximate Amino Acid Probabilities with Biased Nucleotide Usage. (PDF)

93. Mona Singh, Bonnie Berger and Peter S. Kim J. Mol. Biol. (1999)290: 1031-1041. LearnCoil-VMF: Computational Evidence for Coiled Coil-like Motifs in Many Viral Membrane-fusion Proteins. (PDF)

92. Christina Redfield, Brenda A. Schulman, Michael A. Milhollen, Peter S. Kim and Christopher M. Dobson Nat. Struct. Biol.(1999) 6: 948-952. a-Lactalbumin Forms a Compact Molten Globule in the Absence of Disulphide Bonds. (PDF)

91. 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. Core Structure of the Envelope Glycoprotein GP2 from Ebola Virus at 1.9 Å Resolution. (PDF)

90. Debra M. Eckert, Vladimir N. Malashkevich, Lily H. Hong, Peter A. Carr and Peter S. Kim Cell (1999) 99: 103-115. Inhibiting HIV-1 Entry: Discovery of D-Peptide Inhibitors that Target the gp41 Coiled-Coil Pocket. (PDF)

89. Lawren C. Wu and Peter S. Kim J. Mol. Biol. (1998) 280: 175-182. A Specific Hydrophobic Core in the a-Lactalbumin Molten Globule. (PDF)

88. Mona Singh, Bonnie Berger, Peter S. Kim, James M. Berger and Andrea G. Cochran Proc. Natl. Acad. Sci. USA (1998) 95: 2738-2743. Computational Learning Reveals Coiled Coil-Like Motifs in Histidine Kinase Linker Domains. (PDF)

87. Martha G. Oakley and Peter S. Kim Biochemistry (1998) 37: 12603-12610. A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil. (PDF)

86. Vladimir N. Malashkevich, David C. Chan, Christine T. Chutkowski and Peter S. Kim Proc. Natl. Acad. Sci. USA (1998) 95: 9134-9139. Crystal Structure of the Simian Immunodeficiency Virus (SIV) gp41 Core: Conserved Helical Interactions Underlie the Broad Inhibitory Activity of gp41 Peptides. (PDF)

85. Pehr B. Harbury, Joseph J. Plecs, Bruce Tidor, Tom Alber and Peter S. Kim Science (1998) 282: 1462-1467. High-Resolution Protein Design with Backbone Freedom. (PDF)

84. Debra M. Eckert, Vladimir N. Malashkevich and Peter S. Kim J. Mol. Biol. (1998) 284: 859-865. Crystal Structure of GCN4-pIQI, a Trimeric Coiled Coil With Buried Polar Residues. (PDF)

83. David C. Chan, Christine T. Chutkowski and Peter S. Kim Proc. Natl. Acad. Sci. USA (1998) 95: 15613-15617. Evidence that a Prominent Cavity in the Coiled Coil of HIV type 1 gp41 is an Attractive Drug Target. (PDF)

82. Lawren C. Wu and Peter S. Kim Proc. Natl. Acad. Sci. USA (1997) 94: 14314-14319. Hydrophobic Sequence Minimization of the a-Lactalbumin Molten Globule. (PDF)

81. Ethan Wolf, Peter S. Kim and Bonnie Berger Protein Science (1997) 6: 1179-1189. MultiCoil: A Program for Predicting Two- and Three-Stranded Coiled Coils. (PDF)

80. 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. Bioactive and Nuclease-Resistant L-DNA Ligand of Vasopressin. (PDF)

79. Brenda A. Schulman, Peter S. Kim, Christopher M. Dobson and Christina Redfield Nat. Struct. Biol. (1997) 4: 630-634. A Residue-Specific NMR View of the Non-Cooperative Unfolding of a Molten Globule.

78. Martha G. Oakley and Peter S. Kim Biochemistry (1997) 36: 2544-2549. Protein Dissection of the Antiparallel Coiled Coil from Escherichia coli Seryl tRNA Synthetase. (PDF)

77. C. James McKnight, Paul T. Matsudaira and Peter S. Kim Nat. Struct. Biol. (1997) 4: 180-184. NMR Structure of the 35-Residue Villin Headpiece Subdomain.

76. Deborah Fass, Robert A. Davey, Christian A. Hamson, Peter S. Kim, James M. Cunningham and James M. Berger Science(1997) 277: 1662-1666. Structure of a Murine Leukemia Virus Receptor-Binding Glycoprotein at 2.0 Angstrom Resolution. (PDF)

75. Deborah Fass, Stephen Blacklow, Peter S. Kim and James M. Berger Nature (1997) 388: 691-693. Molecular Basis of Familial Hypercholesterolaemia from Structure of LDL Receptor Module. (PDF)

74. David C. Chan, Deborah Fass, James M. Berger and Peter S. Kim Cell (1997) 89: 263-273. Core Structure of gp41 from the HIV Envelope Glycoprotein. (PDF)

73. Chavela M. Carr, Charu Chaudhry and Peter S. Kim Proc. Natl. Acad. Sci. USA (1997) 94: 14306-14313. Influenza Hemagglutinin is Spring-Loaded by a Metastable Native Conformation. (PDF)

72. Lawren C. Wu, Brenda A. Schulman, Zheng-yu Peng and Peter S. Kim Biochemistry (1996) 35: 859-863. Disulfide Determinants of Calcium-Induced Packing in a-Lactalbumin. (PDF)

71. 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. Identification of D-Peptide Ligands through Mirror-Image Phage Display. (PDF)

70. Brenda A. Schulman and Peter S. Kim Nature Structural Biology (1996) 3: 682-687. Proline Scanning Mutagenesis of a Molten Globule Reveals Non-Cooperative Formation of a Protein’s Overall Topology. (PDF)

69. Daniel L. Minor, Jr. and Peter S. Kim Nature (1996) 380: 730-734. Context-Dependent Secondary Structure Formation of a Designed Protein Sequence. (PDF)

68. C. James McKnight, Don S. Doering, Paul T. Matsudaira and Peter S. Kim J. Mol. Biol. (1996) 260: 126-134. A Thermostable 35-Residue Subdomain within Villin Headpiece. (PDF)

67. Kevin J. Lumb and Peter S. Kim Science (1996) 271: 1136-1138. Interhelical Salt Bridges, Coiled-Coil Stability, and Specificity of Dimerization: Response. (PDF)

66. Deborah Fass, Stephen C. Harrison and Peter S. Kim Nat. Struct. Biol. (1996) 3: 465-469. Retrovirus Envelope Domain at 1.7 Å Resolution. (PDF)