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AmberTools.
Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O'Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE 3rd, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM Jr. Case DA, et al. J Chem Inf Model. 2023 Oct 23;63(20):6183-6191. doi: 10.1021/acs.jcim.3c01153. Epub 2023 Oct 8. J Chem Inf Model. 2023. PMID: 37805934 Free PMC article.
Crustwater: Modeling Hydrophobic Solvation.
Yadav AK, Bandyopadhyay P, Coutsias EA, Dill KA. Yadav AK, et al. J Phys Chem B. 2022 Aug 18;126(32):6052-6062. doi: 10.1021/acs.jpcb.2c02695. Epub 2022 Aug 4. J Phys Chem B. 2022. PMID: 35926838 Free PMC article.
Protein storytelling through physics.
Brini E, Simmerling C, Dill K. Brini E, et al. Science. 2020 Nov 27;370(6520):eaaz3041. doi: 10.1126/science.aaz3041. Science. 2020. PMID: 33243857 Free PMC article. Review.
Side-chain Packing Using SE(3)-Transformer.
Jindal A, Kotelnikov S, Padhorny D, Kozakov D, Zhu Y, Chowdhury R, Vajda S. Jindal A, et al. Pac Symp Biocomput. 2022;27:46-55. Pac Symp Biocomput. 2022. PMID: 34890135 Free PMC article.
Simple Model of Liquid Water Dynamics.
Urbic T, Dill KA. Urbic T, et al. J Phys Chem B. 2023 Sep 21;127(37):7996-8001. doi: 10.1021/acs.jpcb.3c05212. Epub 2023 Sep 6. J Phys Chem B. 2023. PMID: 37672327 Free PMC article.
High Accuracy Prediction of PROTAC Complex Structures.
Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. Ignatov M, et al. J Am Chem Soc. 2023 Apr 5;145(13):7123-7135. doi: 10.1021/jacs.2c09387. Epub 2023 Mar 24. J Am Chem Soc. 2023. PMID: 36961978 Free PMC article.
The Protein Folding Problem: The Role of Theory.
Nassar R, Dignon GL, Razban RM, Dill KA. Nassar R, et al. J Mol Biol. 2021 Oct 1;433(20):167126. doi: 10.1016/j.jmb.2021.167126. Epub 2021 Jul 3. J Mol Biol. 2021. PMID: 34224747 Free PMC article. Review.
Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.
Paul I, Bolzan D, Youssef A, Gagnon KA, Hook H, Karemore G, Oliphant MUJ, Lin W, Liu Q, Phanse S, White C, Padhorny D, Kotelnikov S, Chen CS, Hu P, Denis GV, Kozakov D, Raught B, Siggers T, Wuchty S, Muthuswamy SK, Emili A. Paul I, et al. Nat Commun. 2023 Feb 8;14(1):688. doi: 10.1038/s41467-023-36122-x. Nat Commun. 2023. PMID: 36755019 Free PMC article.
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