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Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase.
Mondal J, Friesner RA, Berne BJ. Mondal J, et al. Among authors: friesner ra. J Chem Theory Comput. 2014 Dec 9;10(12):5696-5705. doi: 10.1021/ct500584n. Epub 2014 Nov 13. J Chem Theory Comput. 2014. PMID: 25516727 Free PMC article.
Ligand binding to protein-binding pockets with wet and dry regions.
Wang L, Berne BJ, Friesner RA. Wang L, et al. Among authors: friesner ra. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1326-30. doi: 10.1073/pnas.1016793108. Epub 2011 Jan 4. Proc Natl Acad Sci U S A. 2011. PMID: 21205906 Free PMC article.
In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) J Am Chem Soc 130:2817-2831] of the popular MM-GBSA approach to binding affinity cal …
In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young …
An experimental and computational analysis of the formation of the terminal nitrido complex (eta3-Cp*)2Mo(N)(N3) by elimination of N2 from Cp*2Mo(N3)2: the barrier to elimination is strongly influenced by the exo versus endo configuration of the azide ligand.
Shin JH, Bridgewater BM, Churchill DG, Baik MH, Friesner RA, Parkin G. Shin JH, et al. Among authors: friesner ra. J Am Chem Soc. 2001 Oct 17;123(41):10111-2. doi: 10.1021/ja011416v. J Am Chem Soc. 2001. PMID: 11592896 No abstract available.
Free Energy Perturbation Calculations of the Thermodynamics of Protein Side-Chain Mutations.
Steinbrecher T, Abel R, Clark A, Friesner R. Steinbrecher T, et al. J Mol Biol. 2017 Apr 7;429(7):923-929. doi: 10.1016/j.jmb.2017.03.002. Epub 2017 Mar 6. J Mol Biol. 2017. PMID: 28279701
Accurate Binding Free Energy Predictions in Fragment Optimization.
Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W. Steinbrecher TB, et al. J Chem Inf Model. 2015 Nov 23;55(11):2411-20. doi: 10.1021/acs.jcim.5b00538. Epub 2015 Oct 21. J Chem Inf Model. 2015. PMID: 26457994
Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations.
Schneebeli ST, Hall ML, Breslow R, Friesner R. Schneebeli ST, et al. J Am Chem Soc. 2009 Mar 25;131(11):3965-73. doi: 10.1021/ja806951r. J Am Chem Soc. 2009. PMID: 19243187 Free PMC article.
Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor.
Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Goldfeld DA, et al. Among authors: friesner ra. J Phys Chem B. 2015 Jan 22;119(3):824-35. doi: 10.1021/jp5053612. Epub 2014 Nov 26. J Phys Chem B. 2015. PMID: 25395044
On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities.
Wang L, Berne BJ, Friesner RA. Wang L, et al. Among authors: friesner ra. Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):1937-42. doi: 10.1073/pnas.1114017109. Epub 2012 Jan 23. Proc Natl Acad Sci U S A. 2012. PMID: 22308365 Free PMC article.
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.
Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Friesner RA, et al. J Med Chem. 2006 Oct 19;49(21):6177-96. doi: 10.1021/jm051256o. J Med Chem. 2006. PMID: 17034125
Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results.
Friesner RA. Friesner RA. Adv Protein Chem. 2005;72:79-104. doi: 10.1016/S0065-3233(05)72003-9. Adv Protein Chem. 2005. PMID: 16581373
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