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Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape.
Starr TN, Czudnochowski N, Zatta F, Park YJ, Liu Z, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, Wojcechowskyj JA, De Marco A, Rosen LE, Zhou J, Montiel-Ruiz M, Kaiser H, Tucker H, Housley MP, di Iulio J, Lombardo G, Agostini M, Sprugasci N, Culap K, Jaconi S, Meury M, Dellota E, Cameroni E, Croll TI, Nix JC, Havenar-Daughton C, Telenti A, Lempp FA, Pizzuto MS, Chodera JD, Hebner CM, Whelan SPJ, Virgin HW, Veesler D, Corti D, Bloom JD, Snell G. Starr TN, et al. Among authors: chodera jd. bioRxiv [Preprint]. 2021 Apr 8:2021.04.06.438709. doi: 10.1101/2021.04.06.438709. bioRxiv. 2021. Update in: Nature. 2021 Sep;597(7874):97-102. doi: 10.1038/s41586-021-03807-6 PMID: 33851154 Free PMC article. Updated. Preprint.
Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance.
López-Ríos de Castro R, Rodríguez-Guerra J, Schaller D, Kimber TB, Taylor C, White JB, Backenköhler M, Payne A, Kaminow B, Pulido I, Singh S, Kramer PL, Pérez-Hernández G, Volkamer A, Chodera JD. López-Ríos de Castro R, et al. Among authors: chodera jd. bioRxiv [Preprint]. 2024 Sep 10:2024.09.10.612176. doi: 10.1101/2024.09.10.612176. bioRxiv. 2024. PMID: 39314436 Free PMC article. Preprint.
OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials.
Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, Rodriguez-Guerra J, Simmonett AC, Singh S, Swails J, Turner P, Wang Y, Zhang I, Chodera JD, Fabritiis G, Markland TE. Eastman P, et al. Among authors: chodera jd. ArXiv [Preprint]. 2023 Nov 29:arXiv:2310.03121v2. ArXiv. 2023. Update in: J Phys Chem B. 2024 Jan 11;128(1):109-116. doi: 10.1021/acs.jpcb.3c06662 PMID: 37986730 Free PMC article. Updated. Preprint.
Benchmarking Cross-Docking Strategies in Kinase Drug Discovery.
Schaller DA, Christ CD, Chodera JD, Volkamer A. Schaller DA, et al. Among authors: chodera jd. J Chem Inf Model. 2024 Dec 9;64(23):8848-8858. doi: 10.1021/acs.jcim.4c00905. Epub 2024 Nov 18. J Chem Inf Model. 2024. PMID: 39558632 Free PMC article.
Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning.
Eastman P, Pritchard BP, Chodera JD, Markland TE. Eastman P, et al. Among authors: chodera jd. J Chem Theory Comput. 2024 Oct 8;20(19):8583-8593. doi: 10.1021/acs.jctc.4c00794. Epub 2024 Sep 25. J Chem Theory Comput. 2024. PMID: 39318326
Machine-learned molecular mechanics force fields from large-scale quantum chemical data.
Takaba K, Friedman AJ, Cavender CE, Behara PK, Pulido I, Henry MM, MacDermott-Opeskin H, Iacovella CR, Nagle AM, Payne AM, Shirts MR, Mobley DL, Chodera JD, Wang Y. Takaba K, et al. Among authors: chodera jd. Chem Sci. 2024 Jun 26;15(32):12861-12878. doi: 10.1039/d4sc00690a. eCollection 2024 Aug 14. Chem Sci. 2024. PMID: 39148808 Free PMC article.
129 results