bioRxiv Channel: Rosetta Commons https://biorxiv.org This feed contains articles for bioRxiv Channel "Rosetta Commons" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2 ]]> https://biorxiv.org/cgi/content/short/2020.06.25.171371v1?rss=1" Mahajan, S. P. Srinivasan, Y. Labonte, J. W. DeLisa, M. P. Gray, J. J. 2020-06-27 doi:10.1101/2020.06.25.171371 Cold Spring Harbor Laboratory Press 2020-06-27 <![CDATA[ Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks ]]> https://biorxiv.org/cgi/content/short/2021.04.04.438423v1?rss=1" Koehler Leman, J. Lyskov, S. Lewis, S. Adolf-Bryfogle, J. Alford, R. F. Barlow, K. Ben-Aharon, Z. Farrell, D. Fell, J. Hansen, W. A. Harmalkar, A. Jeliazkov, J. Krys, J. D. Kuenze, G. Ljubetic, A. Loshbaugh, A. L. Maguire, J. Moretti, R. Mulligan, V. K. Nguyen, P. T. OConchuir, S. Roy Burman, S. S. Smith, S. T. Teets, F. Tiemann, J. K. Watkins, A. Woods, H. Yachnin, B. J. Bahl, C. D. Bailey-Kellogg, C. Baker, D. Das, R. DiMaio, F. Khare, S. D. Kortemme, T. Labonte, J. W. Lindorff-Larsen, K. Meiler, J. Schief, W. Schueler-Furman, O. Siegel, J. Stein, A. 2021-04-05 doi:10.1101/2021.04.04.438423 Cold Spring Harbor Laboratory Press 2021-04-05 <![CDATA[ Diverse scientific benchmarks for implicit membrane energy functions ]]> https://biorxiv.org/cgi/content/short/2020.06.23.168021v1?rss=1" Alford, R. F. Gray, J. J. 2020-06-24 doi:10.1101/2020.06.23.168021 Cold Spring Harbor Laboratory Press 2020-06-24 <![CDATA[ Robustification of RosettaAntibody and Rosetta SnugDock ]]> https://biorxiv.org/cgi/content/short/2020.05.26.116210v1?rss=1" Jeliazkov, J. R. Frick, R. Zhou, J. Gray, J. J. 2020-05-26 doi:10.1101/2020.05.26.116210 Cold Spring Harbor Laboratory Press 2020-05-26 <![CDATA[ Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures ]]> https://biorxiv.org/cgi/content/short/2020.02.09.940254v1?rss=1" Ruffolo, J. A. Guerra, C. Mahajan, S. P. Sulam, J. Gray, J. J. 2020-02-10 doi:10.1101/2020.02.09.940254 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ PRosettaC: Rosetta based modeling of PROTAC mediated ternary complexes ]]> https://biorxiv.org/cgi/content/short/2020.05.27.119354v1?rss=1" Zaidman, D. London, N. 2020-05-30 doi:10.1101/2020.05.27.119354 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Design of proteins presenting discontinuous functional sites using deep learning ]]> https://biorxiv.org/cgi/content/short/2020.11.29.402743v1?rss=1" Tischer, D. Lisanza, S. Wang, J. Dong, R. Anishchenko, I. K. Milles, L. Ovchinnikov, S. Baker, D. 2020-11-29 doi:10.1101/2020.11.29.402743 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Protein structure prediction and design in a biologically-realistic implicit membrane ]]> https://biorxiv.org/cgi/content/short/630715v1?rss=1" Alford, R. F. Fleming, P. J. Fleming, K. G. Gray, J. J. 2019-05-08 doi:10.1101/630715 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Designing Peptides on a Quantum Computer ]]> https://biorxiv.org/cgi/content/short/752485v1?rss=1" Mulligan, V. K. Melo, H. Merritt, H. I. Slocum, S. Weitzner, B. D. Watkins, A. M. Renfrew, P. D. Pelissier, C. Arora, P. S. Bonneau, R. 2019-09-02 doi:10.1101/752485 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking ]]> https://biorxiv.org/cgi/content/short/618603v1?rss=1" Pavlovicz, R. E. Park, H. DiMaio, F. 2019-04-25 doi:10.1101/618603 Cold Spring Harbor Laboratory Press 2019-04-25 <![CDATA[ FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds ]]> https://biorxiv.org/cgi/content/short/764449v1?rss=1" Das, R. Watkins, A. M. 2019-09-10 doi:10.1101/764449 Cold Spring Harbor Laboratory Press 2019-09-10 <![CDATA[ Prediction of protein mutational free energy: benchmark and sampling improvements increase classification accuracy ]]> https://biorxiv.org/cgi/content/short/2020.03.18.989657v1?rss=1" Frenz, B. Lewis, S. King, I. Park, H. DiMaio, F. Song, Y. 2020-03-20 doi:10.1101/2020.03.18.989657 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ De novo protein design by deep network hallucination ]]> https://biorxiv.org/cgi/content/short/2020.07.22.211482v1?rss=1" Anishchenko, I. Chidyausiku, T. M. Ovchinnikov, S. Pellock, S. J. Baker, D. 2020-07-23 doi:10.1101/2020.07.22.211482 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints ]]> https://biorxiv.org/cgi/content/short/597872v1?rss=1" Kuenze, G. Bonneau, R. Koehler Leman, J. Meiler, J. 2019-04-03 doi:10.1101/597872 Cold Spring Harbor Laboratory Press 2019-04-03 <![CDATA[ Large-scale design and refinement of stable proteins using sequence-only models ]]> https://biorxiv.org/cgi/content/short/2021.03.12.435185v1?rss=1" Singer, J. M. Novotney, S. Strickland, D. Haddox, H. K. Leiby, N. Rocklin, G. J. Chow, C. M. Roy, A. Bera, A. K. Motta, F. C. Cao, L. Strauch, E.-M. Chidyausiku, T. M. Ford, A. Ho, E. Mackenzie, C. O. Eramian, H. DiMaio, F. Grigoryan, G. Vaughn, M. Stewart, L. J. Baker, D. Klavins, E. 2021-03-12 doi:10.1101/2021.03.12.435185 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Sampling of Structure and Sequence Space of Small Protein Folds ]]> https://biorxiv.org/cgi/content/short/2021.03.10.434454v1?rss=1" Linsky, T. W. Noble, K. Tobin, A. Crow, R. Carter, L. P. Urbauer, J. L. Baker, D. Strauch, E.-M. 2021-03-11 doi:10.1101/2021.03.10.434454 Cold Spring Harbor Laboratory Press 2021-03-11 <![CDATA[ Single Layers of Attention Suffice to Predict Protein Contacts ]]> https://biorxiv.org/cgi/content/short/2020.12.21.423882v1?rss=1" Bhattacharya, N. Thomas, N. Rao, R. Daupras, J. Koo, P. Baker, D. Song, Y. S. Ovchinnikov, S. 2020-12-22 doi:10.1101/2020.12.21.423882 Cold Spring Harbor Laboratory Press 2020-12-22 <![CDATA[ Improved protein structure refinement guided by deep learning based accuracy estimation ]]> https://biorxiv.org/cgi/content/short/2020.07.17.209643v1?rss=1" Hiranuma, N. Park, H. Anishchanka, I. Baek, M. Baker, D. 2020-07-19 doi:10.1101/2020.07.17.209643 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ De novo design of transmembrane beta-barrels ]]> https://biorxiv.org/cgi/content/short/2020.10.22.346965v1?rss=1" Vorobieva, A. A. White, P. Liang, B. Horne, J. E. Bera, A. K. Chow, C. M. Gerben, S. R. Marx, S. Kang, A. Stiving, A. Q. Harvey, S. R. Marx, D. C. Khan, N. Fleming, K. G. Wysocki, V. H. Brockwell, D. J. Tamm, L. K. Radford, S. E. Baker, D. 2020-10-23 doi:10.1101/2020.10.22.346965 Cold Spring Harbor Laboratory Press 2020-10-23 <![CDATA[ Learning a force field from small-molecule crystal lattice predictions enables consistent sub-Angstrom protein-ligand docking ]]> https://biorxiv.org/cgi/content/short/2020.09.06.285239v1?rss=1" Park, H. Zhou, G. Baek, M. Baker, D. DiMaio, F. 2020-09-07 doi:10.1101/2020.09.06.285239 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks ]]> https://biorxiv.org/cgi/content/short/2020.07.27.221333v1?rss=1" Hsia, Y. Mout, R. Sheffler, W. Edman, N. I. Vulovic, I. Park, Y.-J. Redler, R. L. Bick, M. J. Bera, A. K. Courbet, A. Kang, A. Brunette, T. Nattermann, U. Tsai, E. Saleem, A. Chow, C. M. Ekiert, D. C. Bhabha, G. Veesler, D. Baker, D. 2020-07-28 doi:10.1101/2020.07.27.221333 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Protein sequence design by explicit energy landscape optimization ]]> https://biorxiv.org/cgi/content/short/2020.07.23.218917v1?rss=1" Norn, C. Wicky, B. I. M. Juergens, D. Liu, S. Kim, D. Koepnick, B. Anishchenko, I. Foldit Players, Baker, D. Ovchinnikov, S. 2020-07-24 doi:10.1101/2020.07.23.218917 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds ]]> https://biorxiv.org/cgi/content/short/2020.06.17.156646v1?rss=1" Coventry, B. Baker, D. 2020-06-17 doi:10.1101/2020.06.17.156646 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ A generative algorithm for de novo design of proteins with diverse pocket structures ]]> https://biorxiv.org/cgi/content/short/2020.03.23.003913v1?rss=1" Basanta, B. Bick, M. J. Bera, A. K. Norn, C. Chow, C. M. Carter, L. P. Goreshnick, I. Dimaio, F. Baker, D. 2020-03-24 doi:10.1101/2020.03.23.003913 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ Antibody structure prediction using interpretable deep learning ]]> https://biorxiv.org/cgi/content/short/2021.05.27.445982v1?rss=1" Ruffolo, J. A. Sulam, J. Gray, J. J. 2021-05-27 doi:10.1101/2021.05.27.445982 Cold Spring Harbor Laboratory Press 2021-05-27 <![CDATA[ Accurate prediction of protein structures and interactions using a 3-track network ]]> https://biorxiv.org/cgi/content/short/2021.06.14.448402v1?rss=1" Baek, M. DiMaio, F. Anishchenko, I. Dauparas, J. Ovchinnikov, S. Lee, G. R. Wang, J. Cong, Q. Kinch, L. N. Schaeffer, R. D. Millan, C. Park, H. Adams, C. Glassman, C. R. DeGiovanni, A. Pereira, J. H. Rodrigues, A. V. van Dijk, A. A. Ebrecht, A. C. Opperman, D. J. Sagmeister, T. Buhlheller, C. Pavkov-Keller, T. Rathinaswamy, M. K. Dalwadi, U. Yip, C. K. Burke, J. E. Garcia, K. C. Grishin, N. V. Adams, P. D. Read, R. J. Baker, D. 2021-06-15 doi:10.1101/2021.06.14.448402 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Epistasis on the stability landscape of de novo TIM barrels explored by a modular design approach ]]> https://biorxiv.org/cgi/content/short/2020.09.29.319103v1?rss=1" Romero-Romero, S. Costas, M. Silva, D.-A. Kordes, S. Rojas-Ortega, E. Guerra, Y. Tapia, C. Shanmugaratnam, S. Rodriguez-Romero, A. Baker, D. HoĢˆcker, B. Fernandez-Velasco, D. A. 2020-10-01 doi:10.1101/2020.09.29.319103 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Designed proteins assemble antibodies into modular nanocages ]]> https://biorxiv.org/cgi/content/short/2020.12.01.406611v1?rss=1" Divine, R. Dang, H. V. Ueda, G. Fallas, J. A. Vulovic, I. Sheffler, W. Saini, S. Zhao, Y. T. Raj, I. X. Morawski, P. A. Jennewein, M. F. Homad, L. J. Wan, Y.-H. Tooley, M. R. Seeger, F. Fahning, M. L. Etemadi, A. Lazarovits, J. Roederer, A. Walls, A. C. Stewart, L. Mazloomi, M. King, N. P. Campbell, D. J. McGuire, A. T. Stamatatos, L. Ruohola-Baker, H. Mathieu, J. Veesler, D. Baker, D. 2020-12-01 doi:10.1101/2020.12.01.406611 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ A memetic algorithm enables global all-atom protein-protein docking with sidechain flexibility ]]> https://biorxiv.org/cgi/content/short/2021.04.12.437963v1?rss=1" Varela, D. Andre, I. 2021-04-13 doi:10.1101/2021.04.12.437963 Cold Spring Harbor Laboratory Press 2021-04-13 <![CDATA[ XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers ]]> https://biorxiv.org/cgi/content/short/2021.05.05.442729v1?rss=1" Maguire, J. B. Grattarola, D. Klyshko, E. Mulligan, V. K. Melo, H. 2021-05-05 doi:10.1101/2021.05.05.442729 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37-45 ]]> https://biorxiv.org/cgi/content/short/749317v1?rss=1" Roy Burman, S. S. Nance, M. L. Jeliazkov, J. R. Labonte, J. W. Lubin, J. H. Biswas, N. Gray, J. J. 2019-08-30 doi:10.1101/749317 Cold Spring Harbor Laboratory Press 2019-08-30 <![CDATA[ Flexible backbone assembly and refinement of symmetrical homomeric complexes ]]> https://biorxiv.org/cgi/content/short/409730v1?rss=1" nView larger version (64K):norg.highwire.dtl.DTLVardef@1e4834borg.highwire.dtl.DTLVardef@167bd2eorg.highwire.dtl.DTLVardef@1b52510org.highwire.dtl.DTLVardef@1945a02_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Roy Burman, S. S. Yovanno, R. A. Gray, J. J. 2018-09-06 doi:10.1101/409730 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets ]]> https://biorxiv.org/cgi/content/short/223511v1?rss=1" Marze, N. A. Roy Burman, S. S. Sheffler, W. Gray, J. J. 2017-11-22 doi:10.1101/223511 Cold Spring Harbor Laboratory Press 2017-11-22