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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: vajda s. Biophys J. 2024 May 15:S0006-3495(24)00325-4. doi: 10.1016/j.bpj.2024.05.011. Online ahead of print. Biophys J. 2024. PMID: 38751115
Low-Temperature Selective Oxidative Dehydrogenation of Cyclohexene by Titania-Supported Nanostructured Pd, Pt, and Pt-Pd Catalytic Films.
Vaidulych M, Yeh LY, Hoehner R, Jašík J, Kadam SA, Vorochta M, Khalakhan I, Hagen J, Vajda Š. Vaidulych M, et al. Among authors: vajda s. J Phys Chem C Nanomater Interfaces. 2024 Feb 16;128(8):3180-3192. doi: 10.1021/acs.jpcc.3c07064. eCollection 2024 Feb 29. J Phys Chem C Nanomater Interfaces. 2024. PMID: 38445016 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, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. Glukhov E, et al. Among authors: vajda s. bioRxiv [Preprint]. 2023 Dec 14:2023.11.29.569310. doi: 10.1101/2023.11.29.569310. bioRxiv. 2023. PMID: 38077000 Free PMC article. 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: vajda s. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
Cyclohexane Oxidative Dehydrogenation on Graphene-Oxide-Supported Cobalt Ferrite Nanohybrids: Effect of Dynamic Nature of Active Sites on Reaction Selectivity.
Kadam SA, Sandoval S, Bastl Z, Simkovičová K, Kvítek L, Jašík J, Olszówka JE, Valtera S, Vaidulych M, Morávková J, Sazama P, Kubička D, Travert A, van Bokhoven JA, Fortunelli A, Kleibert A, Kalbáč M, Vajda Š. Kadam SA, et al. Among authors: vajda s. ACS Catal. 2023 Oct 5;13(20):13484-13505. doi: 10.1021/acscatal.3c02592. eCollection 2023 Oct 20. ACS Catal. 2023. PMID: 37881789 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: vajda s. Proteins. 2023 Dec;91(12):1822-1828. doi: 10.1002/prot.26587. Epub 2023 Sep 11. Proteins. 2023. PMID: 37697630
Improved prediction of MHC-peptide binding using protein language models.
Hashemi N, Hao B, Ignatov M, Paschalidis IC, Vakili P, Vajda S, Kozakov D. Hashemi N, et al. Among authors: vajda s. Front Bioinform. 2023 Aug 17;3:1207380. doi: 10.3389/fbinf.2023.1207380. eCollection 2023. Front Bioinform. 2023. PMID: 37663788 Free PMC article.
267 results