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Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45.
Proteins. 2020 Aug;88(8):1037-1049. doi: 10.1002/prot.25871. Epub 2020 Jan 6.
Proteins. 2020.
PMID: 31891416
Free PMC article.
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R.
Leman JK, et al. Among authors: khramushin a.
Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1.
Nat Methods. 2020.
PMID: 32483333
Free PMC article.
Review.
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Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures.
Badaczewska-Dawid AE, Khramushin A, Kolinski A, Schueler-Furman O, Kmiecik S.
Badaczewska-Dawid AE, et al. Among authors: khramushin a.
Methods Mol Biol. 2020;2165:273-287. doi: 10.1007/978-1-0716-0708-4_16.
Methods Mol Biol. 2020.
PMID: 32621231
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Harnessing protein folding neural networks for peptide-protein docking.
Tsaban T, Varga JK, Avraham O, Ben-Aharon Z, Khramushin A, Schueler-Furman O.
Tsaban T, et al. Among authors: khramushin a.
Nat Commun. 2022 Jan 10;13(1):176. doi: 10.1038/s41467-021-27838-9.
Nat Commun. 2022.
PMID: 35013344
Free PMC article.
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Matching protein surface structural patches for high-resolution blind peptide docking.
Khramushin A, Ben-Aharon Z, Tsaban T, Varga JK, Avraham O, Schueler-Furman O.
Khramushin A, et al.
Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2121153119. doi: 10.1073/pnas.2121153119. Epub 2022 Apr 28.
Proc Natl Acad Sci U S A. 2022.
PMID: 35482919
Free PMC article.
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A unique PRDM13-associated variant in a Georgian Jewish family with probable North Carolina macular dystrophy and the possible contribution of a unique CFH variant.
Namburi P, Khateb S, Meyer S, Bentovim T, Ratnapriya R, Khramushin A, Swaroop A, Schueler-Furman O, Banin E, Sharon D.
Namburi P, et al. Among authors: khramushin a.
Mol Vis. 2020 Apr 16;26:299-310. eCollection 2020.
Mol Vis. 2020.
PMID: 32476814
Free PMC article.
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Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin.
Ali M, Khramushin A, Yadav VK, Schueler-Furman O, Ivarsson Y.
Ali M, et al. Among authors: khramushin a.
Biochemistry. 2023 Jun 6;62(11):1594-1607. doi: 10.1021/acs.biochem.3c00096. Epub 2023 May 24.
Biochemistry. 2023.
PMID: 37224425
Free PMC article.
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