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Novel procedure for modeling ligand/receptor induced fit effects.
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Sherman W, et al. J Med Chem. 2006 Jan 26;49(2):534-53. doi: 10.1021/jm050540c. J Med Chem. 2006. PMID: 16420040
Docking covalent inhibitors: a parameter free approach to pose prediction and scoring.
Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E. Zhu K, et al. J Chem Inf Model. 2014 Jul 28;54(7):1932-40. doi: 10.1021/ci500118s. Epub 2014 Jun 26. J Chem Inf Model. 2014. PMID: 24916536
Ab initio structure prediction of the antibody hypervariable H3 loop.
Zhu K, Day T. Zhu K, et al. Proteins. 2013 Jun;81(6):1081-9. doi: 10.1002/prot.24240. Epub 2013 May 2. Proteins. 2013. PMID: 23255066
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. van Zundert GCP, et al. J Med Chem. 2018 Dec 27;61(24):11183-11198. doi: 10.1021/acs.jmedchem.8b01292. Epub 2018 Dec 6. J Med Chem. 2018. PMID: 30457858 Free PMC article.
Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling.
Sindhikara D, Spronk SA, Day T, Borrelli K, Cheney DL, Posy SL. Sindhikara D, et al. J Chem Inf Model. 2017 Aug 28;57(8):1881-1894. doi: 10.1021/acs.jcim.7b00052. Epub 2017 Aug 8. J Chem Inf Model. 2017. PMID: 28727915
A hierarchical approach to all-atom protein loop prediction.
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. Jacobson MP, et al. Proteins. 2004 May 1;55(2):351-67. doi: 10.1002/prot.10613. Proteins. 2004. PMID: 15048827
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