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Page 1
Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming.
Lawton ML, Inge MM, Blum BC, Smith-Mahoney EL, Bolzan D, Lin W, McConney C, Porter J, Moore J, Youssef A, Tharani Y, Varelas X, Denis GV, Wong WW, Padhorny D, Kozakov D, Siggers T, Wuchty S, Snyder-Cappione J, Emili A. Lawton ML, et al. Among authors: padhorny d. PLoS Biol. 2024 Dec 17;22(12):e3002943. doi: 10.1371/journal.pbio.3002943. eCollection 2024 Dec. PLoS Biol. 2024. PMID: 39689157 Free PMC article.
MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction.
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Patsahan T, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: padhorny d. Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011. Epub 2024 May 15. Biophys J. 2024. PMID: 38751115
MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: padhorny d. bioRxiv [Preprint]. 2023 Dec 14:2023.11.29.569310. doi: 10.1101/2023.11.29.569310. bioRxiv. 2023. Update in: Biophys J. 2024 Sep 3;123(17):2902-2909. doi: 10.1016/j.bpj.2024.05.011 PMID: 38077000 Free PMC article. Updated. Preprint.
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Vela… See abstract for full author list ➔ Lensink MF, et al. Among authors: padhorny d. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server.
Kotelnikov S, Ashizawa R, Popov KI, Khan O, Ignatov M, Li SX, Hassan M, Coutsias EA, Poda G, Padhorny D, Tropsha A, Vajda S, Kozakov D. Kotelnikov S, et al. Among authors: padhorny d. Proteins. 2023 Dec;91(12):1822-1828. doi: 10.1002/prot.26587. Epub 2023 Sep 11. Proteins. 2023. PMID: 37697630 Free PMC article.
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Paul I, et al. Among authors: padhorny d. Nat Commun. 2023 Feb 8;14(1):688. doi: 10.1038/s41467-023-36122-x. Nat Commun. 2023. PMID: 36755019 Free PMC article.
Opinion: Protein folds vs. protein folding: Differing questions, different challenges.
Chen SJ, Hassan M, Jernigan RL, Jia K, Kihara D, Kloczkowski A, Kotelnikov S, Kozakov D, Liang J, Liwo A, Matysiak S, Meller J, Micheletti C, Mitchell JC, Mondal S, Nussinov R, Okazaki KI, Padhorny D, Skolnick J, Sosnick TS, Stan G, Vakser I, Zou X, Rose GD. Chen SJ, et al. Among authors: padhorny d. Proc Natl Acad Sci U S A. 2023 Jan 3;120(1):e2214423119. doi: 10.1073/pnas.2214423119. Epub 2022 Dec 29. Proc Natl Acad Sci U S A. 2023. PMID: 36580595 Free PMC article. No abstract available.
27 results