Selected Publications


Miller JA, Khatib F, Hammond H, CooperS, Horowitz S. Introducing Foldit Education Mode. Nature Structural & Molecular Biology (2020). https://doi.org/10.1038/s41594-020-0485-6. Click here for PDF


Leman JK, Weitzner BD, Lewis SM. et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods (2020) https://doi.org/10.1038/s41592-020-0848-2. Click here for PDF


Khatib FDesfosses A, Players F, Koepnick B, Flatten J, Popović Z, Baker D, Cooper S, Gutsche I, Horowitz S. Building de novo cryo-electron microscopy structures collaboratively with citizen scientists. PLOS Biology (2019) 17(11):e3000472. Click here for PDF


Koepnick B, Flatten J, Husain T, Ford A, Silva DA, Bick M, Bauer A, Liu G, Ishida Y, Boykov A, Estep RD, Kleinfelter S, Wei L, Players F, Montelione GT, Popović Z, Khatib F Cooper S, Baker D. De novo protein design by citizen scientists. Nature (2019) 570:390–394. Click here for PDF



Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot L, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi A, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem AC, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli S. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports, (2018) 8:9939. Click here for PDF


Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F Cooper S. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics, (2017) 33(17): 2765-2767. Click here for PDF


Horowitz S, Koepnick B, Martin R, Tymieniecki A, Winburn A, Cooper S, Flatten J, Rogawski D, Koropatkin N, Hailu T, Jain N, Koldewey P, Ahlstrom L, Chapman M, Sikkema A, Skiba M, Maloney F, Beinlich F, Players F, UMich S, Popović Z, Baker D, Khatib F Bardwell J. Determining crystal structures through crowdsourcing and coursework. Nature Communications, (2016) 7(12549).
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Rashid M, Khatib F T Hoque, A Sattar. An Enhanced Genetic Algorithm for Ab initio Protein Structure Prediction. IEEE Transactions on Evolutionary Computation, (2015) Volume PP(99). Click here for PDF


Khoury G, Liwo A, Khatib F Zhou H, Chopra G, Bacardit B, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem ACB, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN, Players F. WeFold: A coopetition for protein structure prediction. Proteins: Structure, Function, and Bioinformatics, (2014) 89(9):1850-1868. Click here for PDF


 Cooper S,  Khatib F  Baker D. Increasing Public Involvement in Structural Biology. Structural Biology, (2013) 21(9):1482-4.
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Eiben CB, Siegel JB, Bale J,  Cooper S,  Khatib F Shen B,  Players F,  Stoddard B,  Popović Z,  Baker D. Increased activity through online game player guided large scale remodeling of a designed Diels-Alderase. Nature Biotechnology, (2012) 30(2):190-2.
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Khatib F, Dimaio F; Foldit Contenders Group; Foldit Void Crushers Group, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D. Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology, (2011) 18(10):1175-7.Click here for PDF


Khatib F, Cooper S, Tyka M, Xu K, Makedon I, Popović Z, Baker D, Players F. Algorithm Discovery by Protein Folding Game Players. Proceedings of the National Academy of Sciences USA, (2011) 108(47):18949-18953.Click here for PDF


Cooper S, Khatib F, Makedon I, Lu H, Barbero J, Baker D, Fogarty J, Popović Z, Players F. Analysis of Social Gameplay Macros in the Foldit Cookbook. In Proceedings of the Sixth international Conference on the Foundations of Digital Games, FDG (2011) 9-14.
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Gilski M, Kazmierczyk M, Krzywda S, Zabranska H, Cooper S, Popović Z, Khatib F, Dimaio F, Thompson J, Baker D, Pichova I, Jaskolski M. High-resolution structure of a retroviral protease folded as a monomer. Acta Crystallographica Section D: Biological Crystallography, (2011) 67(11):907-914.Click here for PDF


Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popović Z, Players F. Predicting protein structures with a multiplayer online game. Nature, (2010) 466(7307):756-60.Click here for PDF


Cooper S, Treuille A, Barbero J, Leaver-Fay A, Tuite K, Khatib F, Snyder AC, Beenen M, Salesin D, Baker D, Popović Z, Players F. The challenge of designing scientific discovery games. In Proceedings of the Fifth international Conference on the Foundations of Digital Games, FDG (2010) 40-47.Click here for PDF


Khatib F, Rohl CA, Karplus K. Pokefind: a novel topological filter for use with protein structure prediction. Bioinformatics, (2009) 25: i281-i288.Click here for PDF


Khatib F, Weirauch MT, Rohl CA. Rapid knot detection and application to protein structure prediction. Bioinformatics, (2006) 22(14): 252-259.Click here for PDF