Khatib Lab

Publications

2025 · Acta Crystallographica Section D

Reconstructing Biological Molecules with Help from Video Gamers

Petrides A, Joosten R, Players F, Khatib F, Horowitz S

doi.org/10.1107/S2059798325008149

2024 · ACM Games: Research and Practice

Feel the Rhythm: A Blind-Accessible Rhythm Game Showcasing a Novel Approach to Accessibility

Mrazik M, Khatib F

doi.org/10.1145/3651278

2023 · The Journal of the Copyright Society (Volume 70)

Answering Question One in Google v. Oracle: The Creativity of Computer Programmers

Clifford RD, Khatib F, Kershaw TC, El-Nasan A

doi.org/10.2139/ssrn.4267334

2022 · Structure

Structure of the divergent human astrovirus MLB capsid spike

Delgado-Cunningham K, López T, Khatib F, Arias T, DuBois RM

doi.org/10.1016/j.str.2022.10.010

2022 · Psychology of Aesthetics, Creativity, and the Arts

An Initial Examination of Computer Programs as Creative Works

Kershaw TC, Clifford RD, Khatib F, El-Nasan A

doi.org/10.1037/aca0000457

2020 · Nature Structural & Molecular Biology

Introducing Foldit Education Mode

Miller JA, Khatib F, Hammond H, Cooper S, Horowitz S

2020 · Nature Methods

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman JK, Weitzner BD, Lewis SM, et.al.

2019 · PLOS Biology

Building de novo cryo-electron microscopy structures collaboratively with citizen scientists

Khatib F, Desfosses A, Players F, Koepnick B, Flatten J, Popović Z, Baker D, Cooper S, Gutsche I, Horowitz S

2019 · Nature

NDe novo protein design by citizen scientists

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

2018 · Scientific Reports

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

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, 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

2017 · Bioinformatics

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S

2016 · Nature Communications

Determining crystal structures through crowdsourcing and coursework

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

2015 · IEEE Transactions on Evolutionary Computation

An Enhanced Genetic Algorithm for Ab initio Protein Structure Prediction

Rashid M, Khatib F, Hoque T, Sattar A

2014 · Proteins: Structure, Function, and Bioinformatics

WeFold: A coopetition for protein structure prediction

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

2013 · Structural Biology

Increasing Public Involvement in Structural Biology

Cooper S, Khatib F, Baker D

2012 · Nature Biotechnology

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Eiben CB, Siegel JB, Bale J, Cooper S, Khatib F, Shen B, Players F, Stoddard B, Popović Z, Baker D

2011 · Nature Structural & Molecular Biology

Crystal structure of a monomeric retroviral protease solved by protein folding game players

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

2011 · Proceedings of the National Academy of Sciences USA

Algorithm Discovery by Protein Folding Game Players

Khatib F, Cooper S, Tyka M, Xu K, Makedon I, Popović Z, Baker D, Players F

2011 · Proceedings of the Sixth international Conference on the Foundations of Digital Games

Analysis of Social Gameplay Macros in the Foldit Cookbook

Cooper S, Khatib F, Makedon I, Lu H, Barbero J, Baker D, Fogarty J, Popović Z, Players F

2011 · Acta Crystallographica Section D: Biological Crystallography

High-resolution structure of a retroviral protease folded as a monomer

Gilski M, Kazmierczyk M, Krzywda S, Zabranska H, Cooper S, Popović Z, Khatib F, Dimaio F, Thompson J, Baker D, Pichova I, Jaskolski M

2010 · Nature

Predicting protein structures with a multiplayer online game

Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popović Z, Players F

2010 · Proceedings of the Fifth international Conference on the Foundations of Digital Games, FDG

The challenge of designing scientific discovery games

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

2009 · Bioinformatics

Pokefind: a novel topological filter for use with protein structure prediction

Khatib F, Rohl CA, Karplus K

2006 · Bioinformatics

Rapid knot detection and application to protein structure prediction

Khatib F, Weirauch MT, Rohl CA