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Publications on NCBI PubMed Publications on Google Scholar underlined: Pierce Lab members 2024Yin R, Pierce BG. (2024)Evaluation of AlphaFold antibody-antigen modeling with implications for improving predictive accuracy. Protein Science, 33:e4865. Article PubMed 2023Dey D, Qing E, He Y, Chen Y, Jennings B, Cohn W, Singh S, Gakhar L, Schnicker NJ, Pierce BG, Whitelegge JP, Doray B, Orban J, Gallagher T, Hasan SS. (2023)A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Nature Communications, 14(1):8358. Article PubMed Mariuzza RA, Wu D, Pierce BG. (2023) Structural basis for T cell recognition of cancer neoantigens and implications for predicting neoepitope immunogenicity. Frontiers in Immunology, 14:1303304. Article PubMed Lensink MF, et al., Yin R, Cheung M, Guest JD, Lee J, Pierce BG, et al., Wodak SJ. (2023) Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins, 91:1658–1683. Article PubMed Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP. (2023) SARS-CoV-2 infection establishes a stable and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using restricted T cell receptors. Nature Communications, 14(1):6725. Article PubMed Metcalf MC, Janus BM, Yin R, Wang R, Guest JD, Pozharski E, Law M, Mariuzza RA, Toth EA, Pierce BG, Fuerst TR, Ofek G. (2023) Structure of engineered hepatitis C virus E1E2 ectodomain in complex with neutralizing antibodies. Nature Communications, 14(1):3980. Article PubMed Yin R, Ribeiro-Filho HV, Lin V, Gowthaman R, Cheung M, Pierce BG. (2023) TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning. Nucleic Acids Research, 51(W1):W569-W576. Article PubMed Wu D, Efimov GA, Bogolyubova AV, Pierce BG, Mariuzza RA. (2023) Structural insights into protection against a SARS-CoV-2 spike variant by T cell receptor diversity. Journal of Biological Chemistry, 299(4):103035. Article PubMed 2022Li Q, Humphries F, Girardin RC, Wallace A, Ejemel M, Amcheslavsky A, McMahon CT, Schiller ZA, Ma Z, Cruz J, Dupuis AP, Payne AF, Maryam A, Yilmaz NK, McDonough KA, Pierce BG, Schiffer CA, Kruse AC, Klempner MS, Cavacini LA, Fitzgerald KA, Yang W. (2022)Mucosal nanobody IgA as inhalable and affordable prophylactic and therapeutic treatment against SARS-CoV-2 and emerging variants Frontiers in Immunology, 13:995412. Article PubMed Yin R, Feng BY, Varshney A, Pierce BG. (2022) Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants Protein Science, 31:e4379. Article PubMed Lee JH, Yin R, Ofek G, Pierce BG. (2022) Structural features of antibody-peptide recognition Frontiers in Immunology, 13:910367. Article PubMed Wang R, Suzuki S, Guest JD, Heller B, Almeda M, Andrianov AK, Marin A, Mariuzza RA, Keck ZY, Foung SKH, Yunus AS, Pierce BG, Toth EA, Ploss A, Fuerst TR. (2022) Induction of broadly neutralizing antibodies using a secreted form of the hepatitis C virus E1E2 heterodimer as a vaccine candidate Proceedings of the National Academy of Sciences USA 119(11):e2112008119. Article PubMed Dey D, Singh S, Khan S, Martin M, Schnicker NJ, Gakhar L, Pierce BG, Hasan SS. (2022) An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking Communications Biology, 5(1):115. Article PubMed Wu D, Gowthaman R, Pierce BG, Mariuzza RA. (2022) T cell receptors (TCRs) employ diverse strategies to target a p53 cancer neoantigen Journal of Biological Chemistry, 298(3):101684. Article PubMed Wu D, Kolesnikov A, Yin R, Guest JD, Gowthaman R, Shmelev A, Serdyuk Y, Dianov DV, Efimov GA, Pierce BG*, Mariuzza RA*. (2022) Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors Nature Communications, 13(1):19. Article PubMed *co-corresponding authors Salas JH, Urbanowicz RA, Guest JD, Frumento N, Figueroa A, Clark KE, Keck Z, Cowton VM, Cole SJ, Patel AH, Fuerst TR, Drummer HE, Major M, Tarr AW, Ball JK, Law M, Pierce BG, Foung SKH, Bailey JR. (2022) An antigenically diverse, representative panel of envelope glycoproteins for HCV vaccine development Gastroenterology, 162(2):562-574. Article PubMed 2021Nedeljković M, Postel S, Pierce BG, Sundberg EJ. (2021)Molecular Determinants of Filament Capping Proteins Required for the Formation of Functional Flagella in Gram-Negative Bacteria Biomolecules 11(10):1397. Article PubMed Yin R, Guest JD, Taherzadeh G, Gowthaman R, Mittra I, Quackenbush J, Pierce BG. (2021) Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants. PLoS Computational Biology 17(9): e1009380. Article PubMed Lensink MF, et al., Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, et al., Wodak SJ. (2021) Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins, 89(12):1800-1823. Article PubMed Mordes JP, Cort L, Liu Z, Eberwine R, Blankenhorn EP, Pierce BG. (2021) T Cell Receptor Genotype and Ubash3a Determine Susceptibility to Rat Autoimmune Diabetes. Genes 12(6):852. Article PubMed Toth EA, Chagas A, Pierce BG, Fuerst TR. (2021) Structural and Biophysical Characterization of the HCV E1E2 Heterodimer for Vaccine Development. Viruses 13(6):1027. Article PubMed Guest JD, Pierce BG. (2021) Structure-Based and Rational Design of a Hepatitis C Virus Vaccine. Viruses 13(5):837. Article PubMed Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. (2021) An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure 29:1-16. Article PubMed Amcheslavsky A, Wallace AL, Ejemel M, Li Q, McMahon CT, Stoppato M, Giuntini S, Schiller ZA, Pondish JR, Toomey JR, Schneider RM, Meisinger J, Heukers R, Kruse AC, Barry EM, Pierce BG, Klempner MS, Cavacini LA, Wang Y. (2021) Anti-CfaE nanobodies provide broad cross-protection against major pathogenic enterotoxigenic Escherichia coli strains, with implications for vaccine design. Scientific Reports 11(1):2751. Article PubMed Guest JD, Wang R, Elkholy KH, Chagas A, Chao KL, Cleveland TE 4th, Kim YC, Keck ZY, Marin A, Yunus AS, Mariuzza RA, Andrianov AK, Toth EA, Foung SKH, Pierce BG*, Fuerst TR*. (2021) Design of a native-like secreted form of the hepatitis C virus E1E2 heterodimer. Proceedings of the National Academy of Sciences USA 118(3):e2015149118. Article PubMed *co-corresponding authors Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. (2021) CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Research 49(D1):D282-D287. Article PubMed Andrianov AK, Marin A, Wang R, Chowdhury A, Agnihotri P, Yunus AS, Pierce BG, Mariuzza RA, Fuerst TR. (2021) In Vivo and In Vitro Potency of Polyphosphazene Immunoadjuvants with Hepatitis C Virus Antigen and the Role of their Supramolecular Assembly. Molecular Pharmaceutics 18(2):726-734. Article PubMed 2020Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. (2020)High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics, 36(22-23):5377–5385. Article PubMed Pierce BG, Keck ZY, Wang R, Lau P, Garagusi K, Elkholy K, Toth EA, Urbanowicz RA, Guest JD, Agnihotri P, Kerzic MC, Marin A, Andrianov AK, Ball JK, Mariuzza RA, Fuerst TR, Foung SKH. (2020) Structure-based design of hepatitis C virus E2 glycoprotein improves serum binding and cross-neutralization. Journal of Virology, 94(22):e00704-20. Article PubMed Wu D, Gallagher DT, Gowthaman R, Pierce BG, Mariuzza RA. (2020) Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen. Nature Communications 11(1):2908. Article PubMed Leman JK, et al., Gowthaman R, et al., Pierce BG, et al., Bonneau R. (2020) Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods 17:665–680. Article PubMed Daniels J, Doukas PG, Martinez Escala, ME, Ringbloom KG, Shih DJH, Yang J, Tegtmeyer K, Park J, Thomas JJ, Selli ME, Altunbulakli C, Gowthaman R, Mo SH, Balaji J, Pease DR, Pro B, Abdulla FR, Shea C, Sahni N, Gru AA, Pierce BG, Louissaint Jr A, Guitart J, Choi J. (2020) Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas. Nature Communications 11, 1806. Article PubMed Gowthaman R, Pierce BG. (2020) Modeling and viewing T cell receptors using TCRmodel and TCR3d. Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology 2120:197-212. Article PubMed Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. (2020) Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins 88(3): 503-513. Article PubMed 2019Lensink MF, et al., Guest JD, Gowthaman R, Pierce BG, et al., Wodak SJ. (2019)Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins, 87(12): 1200-1221. Article PubMed Roy Chowdhury I, Yeddula SGR, Pierce BG, Samal SK, Kim SH. (2019) Newcastle disease virus vectors expressing consensus sequence of the H7 HA protein protect broiler chickens and turkeys against highly pathogenic H7N8 virus. Vaccine 37(35): 4956-4962. Article PubMed Gowthaman R, Pierce BG. (2019) TCR3d: The T cell receptor structural repertoire database. Bioinformatics, 35(24): 5323-5325. Article PubMed Keck ZY, Pierce BG, Lau P, Lu J, Wang Y, Underwood A, Bull RA, Prentoe J, Velázquez-Moctezuma R, Walker MR, Luciani F, Guest JD, Fauvelle C, Baumert TF, Bukh J, Lloyd AR, Foung SKH (2019) Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis C virus infections uncover molecular determinants for E2 targeting and vaccine design. PLoS Pathogens 15(5): e1007772. Article PubMed Urbanowicz RA, Wang R, Schiel JE, Keck ZY, Kerzic MC, Rangarajan S, Garagusi KJ, Guest JD, Ball JK, Pierce BG, Mariuzza RA, Foung SKH, Fuerst TR (2019) Antigenicity and Immunogenicity of Differentially Glycosylated HCV E2 Envelope Proteins Expressed in Mammalian and Insect Cells. Journal of Virology 93(7): e01403-18. Article PubMed Lin S, Yang S, He J, Guest JD, Ma Z, Yang L, Pierce BG, Tang Q, Zhang YJ (2019) Zika virus NS5 protein antagonizes type I interferon production via blocking TBK1 activation. Virology 527:180-187. Article PubMed 2018Rangarajan S, He Y, Chen Y, Kerzic MC, Ma B, Gowthaman R, Pierce BG, Nussinov R, Mariuzza RA, Orban J. (2018)Peptide-MHC (pMHC) binding to a human antiviral T cell receptor induces long-range allosteric communication between pMHC- and CD3-binding sites. Journal of Biological Chemistry 293(41):15991-16005. Article PubMed Gowthaman R, Pierce BG. (2018) TCRmodel: high resolution modeling of T cell receptors from sequence. Nucleic Acids Research 46: W396-W401. Article PubMed Guest JD, Pierce BG. (2018) Computational modeling of hepatitis C virus envelope glycoprotein structure and recognition. Frontiers in Immunology 9:1117. Article PubMed Keck ML, Wrensch F, Pierce BG, Baumert TF, Foung SKH. (2018) Mapping determinants of virus neutralization and viral escape for rational design of a hepatitis C virus vaccine. Frontiers in Immunology 9:1194. Article PubMed Fuerst TR, Pierce BG, Keck ZY, Foung SKH. (2018) Designing a B Cell-Based Vaccine against a Highly Variable Hepatitis C Virus. Frontiers in Microbiology 8:2692. Article PubMed 2017Pierce BG, Boucher EN, Piepenbrink KH, Ejemel M, Rapp CA, Thomas WD Jr, Sundberg EJ, Weng Z, Wang Y. (2017)Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope. Journal of Virology 91(20):e01032-17. Article PubMed Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. (2017) ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins 85(5):908-916. Article PubMed Vreven T, Pierce BG, Borrman TM, Weng Z. (2017) Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins 85(3):408-416. Article PubMed 2016Pierce BG, Keck ZY, Lau P, Fauvelle C, Gowthaman R, Baumert TF, Fuerst TR, Mariuzza RA, Foung SK. (2016)Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design. Proceedings of the National Academy of Sciences USA 113(45): E6946-E6954. Article PubMed Keck ZY, Wang Y, Lau P, Lund G, Rangarajan S, Fauvelle C, Liao GC, Holtsberg FW, Warfield KL, Aman MJ, Pierce BG, Fuerst TR, Bailey JR, Baumert TF, Mariuzza RA, Kneteman NM, Foung SK. (2016) Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice. Hepatology 64(6):1922-1933. Article PubMed Pierce BG, Keck ZY, Foung SK. (2016) Viral evasion and challenges of hepatitis C virus vaccine development. Current Opinion in Virology 20:55-63. Article PubMed Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Engineering Design and Selection 29(12):595-606. Article PubMed Fauvelle C, Colpitts CC, Keck ZY, Pierce BG, Foung SK, Baumert TF. Hepatitis C virus vaccine candidates inducing protective neutralizing antibodies. Expert Review of Vaccines 15(12):1535-1544. Article PubMed Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins 84(S1):323-48. Article PubMed Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM. Computational Modeling of T Cell Receptor Complexes. Methods in Molecular Biology 1414:319-40. Article PubMed Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z. Computational Reprogramming of T Cell Antigen Receptor Binding Properties. Methods in Molecular Biology 1414:305-18. Article PubMed Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, Baker BM. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proceedings of the National Academy of Sciences USA 113(9):E1276-85. Article PubMed 2015Yang X, Gao M, Chen G, Pierce BG, Lu J, Weng NP, Mariuzza RA.Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope. Journal of Biological Chemistry 290(48):29106-19. Article PubMed Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology 427(19):3031-41. Article PubMed Li Y, Pierce BG, Wang Q, Keck ZY, Fuerst TR, Foung SK, Mariuzza RA. Structural basis for penetration of the glycan shield of hepatitis C virus E2 glycoprotein by a broadly neutralizing human antibody. Journal of Biological Chemistry 290(16):10117-25. Article PubMed 2014 and beforeCasaz P, Boucher E, Wollacott R, Pierce BG, Rivera R, Sedic M, Ozturk S, Thomas WD Jr, Wang Y.Resolving self-association of a therapeutic antibody by formulation optimization and molecular approaches. MAbs. 2014;6(6):1533-9. doi: 10.4161/19420862.2014.975658. PubMed PMID: 25484044; PubMed Central PMCID: PMC4623042. Pierce BG, Vreven T, Weng Z. Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. BMC Bioinformatics. 2014 Sep 26;15:319. doi: 10.1186/1471-2105-15-319. PubMed PMID: 25260513; PubMed Central PMCID: PMC4261541. Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. PLoS One. 2014 Jun 23;9(6):e100325. doi: 10.1371/journal.pone.0100325. eCollection 2014. PubMed PMID: 24956119; PubMed Central PMCID: PMC4067308. Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proc Natl Acad Sci U S A. 2014 May 6;111(18):6714-9. doi: 10.1073/pnas.1322908111. Epub 2014 Apr 21. PubMed PMID: 24753590; PubMed Central PMCID: PMC4020096. Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol. 2014 Feb 13;10(2):e1003478. doi: 10.1371/journal.pcbi.1003478. eCollection 2014 Feb. PubMed PMID: 24550723; PubMed Central PMCID: PMC3923660. Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014 Jun 15;30(12):1771-3. doi: 10.1093/bioinformatics/btu097. Epub 2014 Feb 14. PubMed PMID: 24532726; PubMed Central PMCID: PMC4058926. Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol. 2014 Apr 3;426(7):1583-99. doi: 10.1016/j.jmb.2013.12.024. Epub 2013 Dec 28. PubMed PMID: 24380763. Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23. PubMed PMID: 24155158; PubMed Central PMCID: PMC4582081. Vreven T, Pierce BG, Hwang H, Weng Z. Performance of ZDOCK in CAPRI rounds 20-26. Proteins. 2013 Dec;81(12):2175-82. doi: 10.1002/prot.24432. PubMed PMID: 24123140; PubMed Central PMCID: PMC3975700. Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23. PubMed PMID: 23843247; PubMed Central PMCID: PMC4143140. Vreven T, Hwang H, Pierce BG, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Brief Bioinform. 2014 Mar;15(2):169-76. doi: 10.1093/bib/bbt047. Epub 2013 Jul 1. PubMed PMID: 23818491; PubMed Central PMCID: PMC3956070. Pierce BG, Eberwine R, Noble JA, Habib M, Shulha HP, Weng Z, Blankenhorn EP, Mordes JP. The Missing Heritability in T1D and Potential New Targets for Prevention. J Diabetes Res. 2013;2013:737485. doi: 10.1155/2013/737485. Epub 2013 Mar 13. PubMed PMID: 23691517; PubMed Central PMCID: PMC3647582. Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. Epub 2012 Nov 29. PubMed PMID: 23203885; PubMed Central PMCID: PMC3531197. Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Sci. 2013 Jan;22(1):35-46. doi: 10.1002/pro.2181. PubMed PMID: 23109003; PubMed Central PMCID: PMC3575858. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112. PubMed PMID: 22955990; PubMed Central PMCID: PMC3431495. Sacha JB, Kim IJ, Chen L, Ullah JH, Goodwin DA, Simmons HA, Schenkman DI, von Pelchrzim F, Gifford RJ, Nimityongskul FA, Newman LP, Wildeboer S, Lappin PB, Hammond D, Castrovinci P, Piaskowski SM, Reed JS, Beheler KA, Tharmanathan T, Zhang N, Muscat-King S, Rieger M, Fernandes C, Rumpel K, Gardner JP 2nd, Gebhard DH, Janies J, Shoieb A, Pierce BG, Trajkovic D, Rakasz E, Rong S, McCluskie M, Christy C, Merson JR, Jones RB, Nixon DF, Ostrowski MA, Loudon PT, Pruimboom-Brees IM, Sheppard NC. Vaccination with cancer- and HIV infection-associated endogenous retrotransposable elements is safe and immunogenic. J Immunol. 2012 Aug 1;189(3):1467-79. doi: 10.4049/jimmunol.1200079. Epub 2012 Jun 27. PubMed PMID: 22745376; PubMed Central PMCID: PMC3401319. Hawse WF, Champion MM, Joyce MV, Hellman LM, Hossain M, Ryan V, Pierce BG, Weng Z, Baker BM. Cutting edge: Evidence for a dynamically driven T cell signaling mechanism. J Immunol. 2012 Jun 15;188(12):5819-23. doi: 10.4049/jimmunol.1200952. Epub 2012 May 18. PubMed PMID: 22611242; PubMed Central PMCID: PMC3375328. Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res. 2012 Oct;22(10):1889-98. doi: 10.1101/gr.139014.112. Epub 2012 Apr 26. PubMed PMID: 22539651; PubMed Central PMCID: PMC3460184. Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci. 2012 Mar;21(3):396-404. doi: 10.1002/pro.2027. Epub 2012 Feb 2. PubMed PMID: 22238219; PubMed Central PMCID: PMC3375440. Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29. PubMed PMID: 22001016; PubMed Central PMCID: PMC3839241. Pierce BG, Hourai Y, Weng Z. Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One. 2011;6(9):e24657. doi: 10.1371/journal.pone.0024657. Epub 2011 Sep 19. PubMed PMID: 21949741; PubMed Central PMCID: PMC3176283. Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. Molecular basis of a million-fold affinity maturation process in a protein-protein interaction. J Mol Biol. 2011 Aug 12;411(2):321-8. doi: 10.1016/j.jmb.2011.06.009. Epub 2011 Jun 12. PubMed PMID: 21689661; PubMed Central PMCID: PMC3143254. Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19. Proteins. 2010 Nov 15;78(15):3104-10. doi: 10.1002/prot.22764. PubMed PMID: 20936681; PubMed Central PMCID: PMC3936321. Han SJ, Hu J, Pierce B, Weng Z, Renne R. (2010) Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins. Journal of General Virology 91(Pt 9):2203-15. Article PubMed Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry. 2010 Aug 24;49(33):7050-9. doi: 10.1021/bi901969a. PubMed PMID: 20681514; PubMed Central PMCID: PMC3062070. Haidar JN, Pierce B, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins. 2009 Mar;74(4):948-60. doi: 10.1002/prot.22203. PubMed PMID: 18767161; PubMed Central PMCID: PMC2696811. Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins. 2008 Nov 15;73(3):705-9. doi: 10.1002/prot.22106. PubMed PMID: 18491384; PubMed Central PMCID: PMC2726780. Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins. 2008 Jul;72(1):270-9. doi: 10.1002/prot.21920. PubMed PMID: 18214977; PubMed Central PMCID: PMC2696687. Wiehe K, Peterson MW, Pierce B, Mintseris J, Weng Z. Protein-protein docking: overview and performance analysis. Methods Mol Biol. 2008;413:283-314. PubMed PMID: 18075170. Bastas G, Sompuram SR, Pierce B, Vani K, Bogen SA. Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies. Mol Cell Proteomics. 2008 Feb;7(2):247-56. Epub 2007 Sep 25. PubMed PMID: 17897933. Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 2007 Dec 1;69(4):719-25. PubMed PMID: 17803212. Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins. 2007 Nov 15;69(3):511-20. PubMed PMID: 17623839. Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins. 2007 Jun 1;67(4):1078-86. PubMed PMID: 17373710. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 2005 Aug 1;60(2):214-6. PubMed PMID: 15981264. Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 2005 Aug 1;60(2):207-13. PubMed PMID: 15981263. Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics. 2005 Apr 15;21(8):1472-8. Epub 2004 Dec 21. PubMed PMID: 15613396. |