Publications | Shourya S. Roy Burman

Li J*, Wang L*, Hahn Q, Nowak R, Viennet T, Orellana E, Roy Burman SS, Yue H, Hunkeler M, Fontana P, Wu H, Arthanari H, Fischer ES & Gregory RI (2023). Structural basis of regulated m7G tRNA modification by METTL1–WDR4. Nature.

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Zhang W*, Roy Burman SS*, Chen J, Donovan KA, Cao Y, Shu C, Zhang B, Zeng Z, Gu S, Zhang Y, Li D, Fischer ES†, Tokheim C† & Liu XS† (2022). Machine learning modeling of protein-intrinsic features predicts tractability of targeted protein degradation. Genomics, Proteomics & Bioinformatics.

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Nitsch L*, Jensen P*, Yoon H, Koeppel J, Roy Burman SS, Fischer ES, Scholl C, Fröhling S & Slabicki M (2022). BTBBCL6 dimers as building blocks for reversible drug-induced protein oligomerization. Cell Reports Methods.

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Meyerhardt JA, Yue H, Nowak RP, Brais L, Ma C, Johnson S, Harrod J, Roy Burman SS, Hendrickson L, Fischinger S, Alter G, Hahn W, Johnson BE & Fischer ES (2022). Serological testing for SARS-CoV-2 antibodies of employees shows low transmission working in a cancer center. PLoS One.

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Koehler Leman J*†, Lyskov S*, Lewis S*, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetic A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nguyen PT, Ó Conchúir S, Roy Burman SS, Smith ST, Teets F, Tiemann JKS, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel J, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ† & Bonneau R† (2021). Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communication.

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Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Roy Burman SS, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, Wu Y, Willis J, Kulp D, Das R, Dunbrack RL Jr, Schief W, Kuhlman B, Siegel JB & Gray JJ (2021). PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. The Biophysicist.

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Slabicki M*, Yoon H*, Koeppel J*, Nitsch L, Roy Burman SS, Di Genua CA, Donovan KA, Sperling AS, Hunkeler M, Tsai JM, Sharma R, Guirguis A, Zou C, Chudasama P, Gasser JA, Miller PG, Scholl C, Fröhling S, Nowak RP, Fischer ES† & Ebert BL† (2020). Small molecule-induced polymerization triggers degradation of BCL6. Nature.

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Roy Burman SS, Jeliazkov JR, Labonte JW, Nance ML, Lubin JH, Biswas N & Gray JJ (2020). Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37–45. Proteins.

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Koehler Leman J, 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 S, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford A, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang P-S, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib Firas, 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, Roy Burman SS, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furma O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel J, Silva D-A, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY-R, Watkins A, Zimmerman L & Bonneau R (2020). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods.

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Roy Burman SS, Yovanno RA & Gray JJ (2019). Flexible backbone assembly and refinement of symmetrical homomeric complexes. Structure.

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Marze NA*, Roy Burman SS*, Sheffler W & Gray JJ (2018). Efficient flexible backbone protein–protein docking for challenging targets. Bioinformatics.

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Kalin JH*, Wu M*, Gomez AV*, Song Y*, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe J†, Mattevi A†, Alani RM† & Cole PA† (2018). Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors. Nature Communications.

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Marze NA*, Jeliazkov JR*, Roy Burman SS, Boyken SE, DiMaio F & Gray JJ (2016). Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28–35. Proteins.

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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 (2016). Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins.

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