Induced fit with replica exchange improves protein complex structure prediction

por Harmalkar, Ameya, Mahajan, Sai Pooja, Gray, Jeffrey J.
Publicado 2022

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

por Chu, Lee-Shin, Ruffolo, Jeffrey A., Harmalkar, Ameya, Gray, Jeffrey J.
Publicado 2023

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

por Cohen-Khait, Ruth, Harmalkar, Ameya, Pham, Phuong, Webby, Melissa N., Housden, Nicholas G., Elliston, Emma, Hopper, Jonathan T. S., Mohammed, Shabaz, Robinson, Carol V., Gray, Jeffrey J., Kleanthous, Colin
Publicado 2021

Toward generalizable prediction of antibody thermostability using machine learning on sequence and structure features

por Harmalkar, Ameya, Rao, Roshan, Richard Xie, Yuxuan, Honer, Jonas, Deisting, Wibke, Anlahr, Jonas, Hoenig, Anja, Czwikla, Julia, Sienz-Widmann, Eva, Rau, Doris, Rice, Austin J., Riley, Timothy P., Li, Danqing, Catterall, Hannah B., Tinberg, Christine E., Gray, Jeffrey J., Wei, Kathy Y.
Publicado 2023

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

por Koehler Leman, Julia, Lyskov, Sergey, Lewis, Steven M., Adolf-Bryfogle, Jared, Alford, Rebecca F., Barlow, Kyle, Ben-Aharon, Ziv, Farrell, Daniel, Fell, Jason, Hansen, William A., Harmalkar, Ameya, Jeliazkov, Jeliazko, Kuenze, Georg, Krys, Justyna D., Ljubetič, Ajasja, Loshbaugh, Amanda L., Maguire, Jack, Moretti, Rocco, Mulligan, Vikram Khipple, Nance, Morgan L., Nguyen, Phuong T., Ó Conchúir, Shane, Roy Burman, Shourya S., Samanta, Rituparna, Smith, Shannon T., Teets, Frank, Tiemann, Johanna K. S., Watkins, Andrew, Woods, Hope, Yachnin, Brahm J., Bahl, Christopher D., Bailey-Kellogg, Chris, Baker, David, Das, Rhiju, DiMaio, Frank, Khare, Sagar D., Kortemme, Tanja, Labonte, Jason W., Lindorff-Larsen, Kresten, Meiler, Jens, Schief, William, Schueler-Furman, Ora, Siegel, Justin B., Stein, Amelie, Yarov-Yarovoy, Vladimir, Kuhlman, Brian, Leaver-Fay, Andrew, Gront, Dominik, Gray, Jeffrey J., Bonneau, Richard
Publicado 2021