De novo design of small beta barrel proteins

por Kim, David E., Jensen, Davin R., Feldman, David, Tischer, Doug, Saleem, Ayesha, Chow, Cameron M., Li, Xinting, Carter, Lauren, Milles, Lukas, Nguyen, Hannah, Kang, Alex, Bera, Asim K., Peterson, Francis C., Volkman, Brian F., Ovchinnikov, Sergey, Baker, David
Publicado 2023

De novo design of a fluorescence-activating β-barrel

por Dou, Jiayi, Vorobieva, Anastassia A., Sheffler, William, Doyle, Lindsey A., Park, Hahnbeom, Bick, Matthew J., Mao, Binchen, Foight, Glenna W., Lee, Min Yen, Gagnon, Lauren A., Carter, Lauren, Sankaran, Banumathi, Ovchinnikov, Sergey, Marcos, Enrique, Huang, Po-Ssu, Vaughan, Joshua C., Stoddard, Barry L., Baker, David
Publicado 2018

Unraveling the functional dark matter through global metagenomics

por Pavlopoulos, Georgios A., Baltoumas, Fotis A., Liu, Sirui, Selvitopi, Oguz, Camargo, Antonio Pedro, Nayfach, Stephen, Azad, Ariful, Roux, Simon, Call, Lee, Ivanova, Natalia N., Chen, I. Min, Paez-Espino, David, Karatzas, Evangelos, Iliopoulos, Ioannis, Konstantinidis, Konstantinos, Tiedje, James M., Pett-Ridge, Jennifer, Baker, David, Visel, Axel, Ouzounis, Christos A., Ovchinnikov, Sergey, Buluç, Aydin, Kyrpides, Nikos C.
Publicado 2023

Scaffolding protein functional sites using deep learning

por Wang, Jue, Lisanza, Sidney, Juergens, David, Tischer, Doug, Watson, Joseph L., Castro, Karla M., Ragotte, Robert, Saragovi, Amijai, Milles, Lukas F., Baek, Minkyung, Anishchenko, Ivan, Yang, Wei, Hicks, Derrick R., Expòsit, Marc, Schlichthaerle, Thomas, Chun, Jung-Ho, Dauparas, Justas, Bennett, Nathaniel, Wicky, Basile I. M., Muenks, Andrew, DiMaio, Frank, Correia, Bruno, Ovchinnikov, Sergey, Baker, David
Publicado 2022

De novo design of protein structure and function with RFdiffusion

por Watson, Joseph L., Juergens, David, Bennett, Nathaniel R., Trippe, Brian L., Yim, Jason, Eisenach, Helen E., Ahern, Woody, Borst, Andrew J., Ragotte, Robert J., Milles, Lukas F., Wicky, Basile I. M., Hanikel, Nikita, Pellock, Samuel J., Courbet, Alexis, Sheffler, William, Wang, Jue, Venkatesh, Preetham, Sappington, Isaac, Torres, Susana Vázquez, Lauko, Anna, De Bortoli, Valentin, Mathieu, Emile, Ovchinnikov, Sergey, Barzilay, Regina, Jaakkola, Tommi S., DiMaio, Frank, Baek, Minkyung, Baker, David
Publicado 2023

A structural biology community assessment of AlphaFold2 applications

por Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M., Davey, Norman E., Stein, Amelie, Elofsson, Arne, Croll, Tristan I., Beltrao, Pedro
Publicado 2022

Accurate prediction of protein structures and interactions using a 3-track neural network

por Baek, Minkyung, DiMaio, Frank, Anishchenko, Ivan, Dauparas, Justas, Ovchinnikov, Sergey, Lee, Gyu Rie, Wang, Jue, Cong, Qian, Kinch, Lisa N., Schaeffer, R. Dustin, Millán, Claudia, Park, Hahnbeom, Adams, Carson, Glassman, Caleb R., DeGiovanni, Andy, Pereira, Jose H., Rodrigues, Andria V., van Dijk, Alberdina A., Ebrecht, Ana C., Opperman, Diederik J., Sagmeister, Theo, Buhlheller, Christoph, Pavkov-Keller, Tea, Rathinaswamy, Manoj K, Dalwadi, Udit, Yip, Calvin K, Burke, John E, Garcia, K. Christopher, Grishin, Nick V., Adams, Paul D., Read, Randy J., Baker, David
Publicado 2021

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

por Keasar, Chen, McGuffin, Liam J., Wallner, Björn, Chopra, Gaurav, Adhikari, Badri, Bhattacharya, Debswapna, Blake, Lauren, Bortot, Leandro Oliveira, Cao, Renzhi, Dhanasekaran, B. K., Dimas, Itzhel, Faccioli, Rodrigo Antonio, Faraggi, Eshel, Ganzynkowicz, Robert, Ghosh, Sambit, Ghosh, Soma, Giełdoń, Artur, Golon, Lukasz, He, Yi, Heo, Lim, Hou, Jie, Khan, Main, Khatib, Firas, Khoury, George A., Kieslich, Chris, Kim, David E., Krupa, Pawel, Lee, Gyu Rie, Li, Hongbo, Li, Jilong, Lipska, Agnieszka, Liwo, Adam, Maghrabi, Ali Hassan A., Mirdita, Milot, Mirzaei, Shokoufeh, Mozolewska, Magdalena A., Onel, Melis, Ovchinnikov, Sergey, Shah, Anand, Shah, Utkarsh, Sidi, Tomer, Sieradzan, Adam K., Ślusarz, Magdalena, Ślusarz, Rafal, Smadbeck, James, Tamamis, Phanourios, Trieber, Nicholas, Wirecki, Tomasz, Yin, Yanping, Zhang, Yang, Bacardit, Jaume, Baranowski, Maciej, Chapman, Nicholas, Cooper, Seth, Defelicibus, Alexandre, Flatten, Jeff, Koepnick, Brian, Popović, Zoran, Zaborowski, Bartlomiej, Baker, David, Cheng, Jianlin, Czaplewski, Cezary, Delbem, Alexandre Cláudio Botazzo, Floudas, Christodoulos, Kloczkowski, Andrzej, Ołdziej, Stanislaw, Levitt, Michael, Scheraga, Harold, Seok, Chaok, Söding, Johannes, Vishveshwara, Saraswathi, Xu, Dong, Crivelli, Silvia N.
Publicado 2018