Channel:  Rosetta Commons

33 Articles

A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and sidechain flexibility
Varela, D., Karlin, V., Andre, I.
10.1101/2021.04.12.437963 — Posted: 2022-03-21
Antibody structure prediction using interpretable deep learning
Ruffolo, J. A., Sulam, J., Gray, J. J.
10.1101/2021.05.27.445982 — Posted: 2021-07-14
Accurate prediction of protein structures and interactions using a 3-track network
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.
10.1101/2021.06.14.448402 — Posted: 2021-06-15
XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
Maguire, J. B., Grattarola, D., Klyshko, E., Mulligan, V. K., Melo, H.
10.1101/2021.05.05.442729 — Posted: 2021-05-05
Large-scale design and refinement of stable proteins using sequence-only models
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.
10.1101/2021.03.12.435185 — Posted: 2021-04-06
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
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.
10.1101/2021.04.04.438423 — Posted: 2021-04-05
The stability landscape of de novo TIM barrels explored by a modular design approach
Romero-Romero, S., Costas, M., Silva, D.-A., Kordes, S., Rojas-Ortega, E., Guerra, Y., Tapia, C., Shanmugaratnam, S., Rodriguez-Romero, A., Baker, D., Höcker, B., Fernandez-Velasco, D. A.
10.1101/2020.09.29.319103 — Posted: 2021-03-15
Sampling of Structure and Sequence Space of Small Protein Folds
Linsky, T. W., Noble, K., Tobin, A., Crow, R., Carter, L. P., Urbauer, J. L., Baker, D., Strauch, E.-M.
10.1101/2021.03.10.434454 — Posted: 2021-03-11
Single Layers of Attention Suffice to Predict Protein Contacts
Bhattacharya, N., Thomas, N., Rao, R., Dauparas, J., Koo, P., Baker, D., Song, Y. S., Ovchinnikov, S.
10.1101/2020.12.21.423882 — Posted: 2020-12-22
Designed proteins assemble antibodies into modular nanocages
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.
10.1101/2020.12.01.406611 — Posted: 2020-12-01

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