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The Journal of Physical Chemistry. B|September 24, 2010
Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water modelsDavid S Cerutti, Lydia Freddolino, Robert E Duke, et al.Biorxiv : the Preprint Server for Biology|January 23, 2024
Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio choleraeYulduz Rakibova, Drew T Dunham, Kimberley D Seed, et al.The Journal of Physical Chemistry. B|August 19, 2007
Assembly of lipids and proteins into lipoprotein particlesAmy Y Shih, Anton Arkhipov, Lydia Freddolino, et al.Biorxiv : the Preprint Server for Biology|June 29, 2026
Whole-proteome structure/function prediction in Uropathogenic E. coli reveals previously missed host-microbe and microbe-phage interaction pathwaysChunxiang Peng, Henry Schreiber, Chengxin Zhang, et al.Nature Methods|January 3, 2024
Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics dataWei Zheng, Qiqige Wuyun, Yang Li, et al.Journal of Chemical Theory and Computation|January 31, 2009
Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen DynamicsDavid S Cerutti, Robert Duke, Lydia Freddolino, et al.Nature Protocols|April 28, 2026
Profiling large-scale protein occupancy on bacterial genomes using IPOD-HRRebecca L Hurto, Jeremy W Schroeder, Julian Trouillon, et al.Nature Communications|September 16, 2023
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure predictionYang Li, Chengxin Zhang, Chenjie Feng, et al.Elife|March 23, 2023
Nutrigenomic regulation of sensory plasticityHayeon Sung, Anoumid Vaziri, Daniel Wilinski, et al.Briefings in Bioinformatics|March 22, 2024
DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fittingZiying Zhang, Yaxian Cai, Biao Zhang, et al.Pageof 9