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Page 1
End-to-end differentiable construction of molecular mechanics force fields.
Wang Y, Fass J, Kaminow B, Herr JE, Rufa D, Zhang I, Pulido I, Henry M, Bruce Macdonald HE, Takaba K, Chodera JD. Wang Y, et al. Among authors: pulido i. Chem Sci. 2022 Sep 8;13(41):12016-12033. doi: 10.1039/d2sc02739a. eCollection 2022 Oct 26. Chem Sci. 2022. PMID: 36349096 Free PMC article.
Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.
Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Zhang I, et al. Among authors: pulido i. bioRxiv [Preprint]. 2023 Jun 21:2023.03.07.530278. doi: 10.1101/2023.03.07.530278. bioRxiv. 2023. Update in: J Chem Theory Comput. 2023 Aug 8;19(15):4863-4882. doi: 10.1021/acs.jctc.3c00333 PMID: 36945557 Free PMC article. Updated. Preprint.
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors.
Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC; COVID Moonshot Consortium‡; Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, Aschenbrenner JC, Balcomb BH, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Bilenko VA, Borden B, Boulet P, Bowman GR, Brewitz L, Brun J, Bvnbs S, Calmiano M, Carbery A, Carney DW, Cattermole E, Chang E, Chernyshenko E, Clyde A, Coffland JE, Cohen G, Cole JC, Contini A, Cox L, Croll TI, Cvitkovic M, De Jonghe S, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett LE, Eastman P, Erez N, Eyermann CJ, Fairhead M, Fate G, Fedorov O, Fernandes RS, Ferrins L, Foster R, Foster H, Fraisse L, Gabizon R, García-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen RC, Glinert I, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Haneef A, Hassell Hart S, Heer J, Henry M, Hill M, Horrell S, Huang QYJ, Huliak VD, Hurley MFD, Israely T, Jajack A, Jansen J, Jnoff E, Jochmans D, John T, Kaminow B, Kang L, Kantsadi AL, Kenny PW, Kiappes JL, Kinakh SO, Kovar B, Krojer T, La VNT, Laghnimi-Hahn S, Lefker BA, Levy H, Lithgo RM, Logvinenko IG, Lukacik P, Macdonald HB, MacLean … See abstract for full author list ➔ Boby ML, et al. Among authors: pulido i. Science. 2023 Nov 10;382(6671):eabo7201. doi: 10.1126/science.abo7201. Epub 2023 Nov 10. Science. 2023. PMID: 37943932 Free PMC article.
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: pulido i. 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.
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: pulido i. bioRxiv [Preprint]. 2024 Sep 10:2024.09.10.612176. doi: 10.1101/2024.09.10.612176. bioRxiv. 2024. PMID: 39314436 Free PMC article. Preprint.
A Contemporary Picture of Coagulase-Negative Staphylococcal Endocarditis: A Nationwide GAMES Cohort Study.
Palom-Grau C, Cuervo G, Muñoz P, Marín Arriaza M, Martínez-Sellés M, González-Ramallo V, de Alarcón A, Poyato-Borrego M, Rodríguez-García R, Rodríguez-Esteban MÁ, Fariñas MC, González-Rico C, Goenaga MÁ, Ojeda-Burgos G, Goikoetxea-Agirre AJ, Calderón-Parra J, López-Azor JC, García-Vázquez E, Loeches B, Quintana E, García de la Mària C, Llopis J, Miró JM; GAMES Investigators. Palom-Grau C, et al. J Am Coll Cardiol. 2024 Oct 25:S0735-1097(24)08573-5. doi: 10.1016/j.jacc.2024.09.027. Online ahead of print. J Am Coll Cardiol. 2024. PMID: 39580721
52 results