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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
Casalino, Lorenzo; Dommer, Abigail C; Gaieb, Zied; Barros, Emilia P; Sztain, Terra; Ahn, Surl-Hee; Trifan, Anda; Brace, Alexander; Bogetti, Anthony T; Clyde, Austin; Ma, Heng; Lee, Hyungro; Turilli, Matteo; Khalid, Syma; Chong, Lillian T; Simmerling, Carlos; Hardy, David J; Maia, Julio Dc; Phillips, James C; Kurth, Thorsten; Stern, Abraham C; Huang, Lei; McCalpin, John D; Tatineni, Mahidhar; Gibbs, Tom; Stone, John E; Jha, Shantenu; Ramanathan, Arvind; Amaro, Rommie E.
Afiliación
  • Casalino L; University of California San Diego, La Jolla, CA, USA.
  • Dommer AC; Authors with symbol indicate equal contribution.
  • Gaieb Z; University of California San Diego, La Jolla, CA, USA.
  • Barros EP; Authors with symbol indicate equal contribution.
  • Sztain T; University of California San Diego, La Jolla, CA, USA.
  • Ahn SH; Authors with symbol indicate equal contribution.
  • Trifan A; University of California San Diego, La Jolla, CA, USA.
  • Brace A; University of California San Diego, La Jolla, CA, USA.
  • Bogetti AT; University of California San Diego, La Jolla, CA, USA.
  • Clyde A; Argonne National Lab, Lemont, IL, USA.
  • Ma H; University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Lee H; Argonne National Lab, Lemont, IL, USA.
  • Turilli M; University of Pittsburgh, Pittsburgh, PA, USA.
  • Khalid S; Argonne National Lab, Lemont, IL, USA.
  • Chong LT; University of Chicago, Chicago, IL, USA.
  • Simmerling C; Argonne National Lab, Lemont, IL, USA.
  • Hardy DJ; Rutgers University, Piscataway, NJ, USA.
  • Maia JD; Rutgers University, Piscataway, NJ, USA.
  • Phillips JC; University of Southampton, Southampton, UK.
  • Kurth T; University of Pittsburgh, Pittsburgh, PA, USA.
  • Stern AC; Stony Brook University, Stony Brook, NY, USA.
  • Huang L; University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • McCalpin JD; University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Tatineni M; University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Gibbs T; NVIDIA Corporation, Santa Clara, CA, USA.
  • Stone JE; NVIDIA Corporation, Santa Clara, CA, USA.
  • Jha S; Texas Advanced Computing Center, Austin, TX, USA.
  • Ramanathan A; Texas Advanced Computing Center, Austin, TX, USA.
  • Amaro RE; San Diego Supercomputing Center, La Jolla, CA, USA.
Int J High Perform Comput Appl ; 35(5): 432-451, 2021 Sep.
Article en En | MEDLINE | ID: mdl-38603008
ABSTRACT
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Int J High Perform Comput Appl Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: Int J High Perform Comput Appl Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos