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PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.
Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp DW, Das R, Dunbrack RL Jr, Schief W, Kuhlman B, Siegel JB, Gray JJ. Le KH, et al. Among authors: kulp dw. Biophysicist (Rockv). 2021 Apr;2(1):108-122. doi: 10.35459/tbp.2019.000147. Epub 2021 Apr 14. Biophysicist (Rockv). 2021. PMID: 35128343 Free PMC article.
Advances in structure-based vaccine design.
Kulp DW, Schief WR. Kulp DW, et al. Curr Opin Virol. 2013 Jun;3(3):322-31. doi: 10.1016/j.coviro.2013.05.010. Epub 2013 Jun 25. Curr Opin Virol. 2013. PMID: 23806515 Free PMC article. Review.
Structure-based design of native-like HIV-1 envelope trimers to silence non-neutralizing epitopes and eliminate CD4 binding.
Kulp DW, Steichen JM, Pauthner M, Hu X, Schiffner T, Liguori A, Cottrell CA, Havenar-Daughton C, Ozorowski G, Georgeson E, Kalyuzhniy O, Willis JR, Kubitz M, Adachi Y, Reiss SM, Shin M, de Val N, Ward AB, Crotty S, Burton DR, Schief WR. Kulp DW, et al. Nat Commun. 2017 Nov 21;8(1):1655. doi: 10.1038/s41467-017-01549-6. Nat Commun. 2017. PMID: 29162799 Free PMC article.
A generalized HIV vaccine design strategy for priming of broadly neutralizing antibody responses.
Steichen JM, Lin YC, Havenar-Daughton C, Pecetta S, Ozorowski G, Willis JR, Toy L, Sok D, Liguori A, Kratochvil S, Torres JL, Kalyuzhniy O, Melzi E, Kulp DW, Raemisch S, Hu X, Bernard SM, Georgeson E, Phelps N, Adachi Y, Kubitz M, Landais E, Umotoy J, Robinson A, Briney B, Wilson IA, Burton DR, Ward AB, Crotty S, Batista FD, Schief WR. Steichen JM, et al. Among authors: kulp dw. Science. 2019 Dec 6;366(6470):eaax4380. doi: 10.1126/science.aax4380. Epub 2019 Oct 31. Science. 2019. PMID: 31672916 Free PMC article.
Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design.
Adolf-Bryfogle J, Labonte JW, Kraft JC, Shapovalov M, Raemisch S, Lütteke T, DiMaio F, Bahl CD, Pallesen J, King NP, Gray JJ, Kulp DW, Schief WR. Adolf-Bryfogle J, et al. Among authors: kulp dw. PLoS Comput Biol. 2024 Jun 24;20(6):e1011895. doi: 10.1371/journal.pcbi.1011895. eCollection 2024 Jun. PLoS Comput Biol. 2024. PMID: 38913746 Free PMC article.
Global site-specific N-glycosylation analysis of HIV envelope glycoprotein.
Cao L, Diedrich JK, Kulp DW, Pauthner M, He L, Park SR, Sok D, Su CY, Delahunty CM, Menis S, Andrabi R, Guenaga J, Georgeson E, Kubitz M, Adachi Y, Burton DR, Schief WR, Yates JR III, Paulson JC. Cao L, et al. Among authors: kulp dw. Nat Commun. 2017 Mar 28;8:14954. doi: 10.1038/ncomms14954. Nat Commun. 2017. PMID: 28348411 Free PMC article.
Precursor Frequency and Affinity Determine B Cell Competitive Fitness in Germinal Centers, Tested with Germline-Targeting HIV Vaccine Immunogens.
Abbott RK, Lee JH, Menis S, Skog P, Rossi M, Ota T, Kulp DW, Bhullar D, Kalyuzhniy O, Havenar-Daughton C, Schief WR, Nemazee D, Crotty S. Abbott RK, et al. Among authors: kulp dw. Immunity. 2018 Jan 16;48(1):133-146.e6. doi: 10.1016/j.immuni.2017.11.023. Epub 2017 Dec 26. Immunity. 2018. PMID: 29287996 Free PMC article.
69 results