Bibliography
[Allerton-2006]
Allerton, C.M.N.; Barber, C.G.; Beaumont, K.C; Brown, D.G.; Cole, S.M.; Ellis, D.; Lane, C.A.L.; Maw, G.N.; et al.
A Novel Series of Potent and Selective PDE5 Inhibitors with Potential for High and Dose-Independent Oral Bioavailability.
J. Med. Chem. 2006, 49 (12), 3581–3594.
DOI: 10.1021/jm060113e
[Card-2004]
Card, G.L.; England, B.P.; Suzuki, Y.; Fong, D.; Powell, B.; Lee, B.; Luu, C.; Tabrizizad, M.; et al.
Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases.
Structure 2004, 12 (12), 2233-2247.
DOI: 10.1016/j.str.2004.10.004
[Gapsys-2020]
Gapsys, V.; Pérez-Benito, L.; Aldeghi, M.; Seeliger, D.; van Vlijmen, H.; Tresadern, G.; de Groot, B.L.
Large Scale Relative Protein Ligand Binding Affinities Using Nonequilibrium Alchemy.
Chem. Sci. 2020, 11 (4), 1140–1152.
DOI: 10.1039/c9sc03754c
[Horton-2022]
Horton, J.T.; Boothroyd, S.; Wagner, J.; Mitchell, J.A.; Gokey, T.; Dotson, D.L.; Behara, P.K.; Ramaswamy, V.K.; Mackey, M.; Chodera, J.D.; Anwar, M.; Mobley, D.L.; Cole, D.J.
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale.
J. Chem. Inf. Model. 2022, 62 (22), 5622–5633.
DOI: 10.1021/acs.jcim.2c01153
[Hummer-2001]
Hummer, G.
Fast-growth thermodynamic integration: Error and efficiency analysis.
J. Chem. Phys. 2001, 114, 7330–7337
DOI: 10.1063/1.1363668
[Hummer-2002]
Hummer, G.
Fast-growth Thermodynamic Integration∶ Results for Sodium Ion Hydration.
Molecular Simulation. 2002, 28 (1-2), 81-90.
DOI: 10.1080/08927020211972
[Jarzynski-1997a]
Jarzynski, C.
Nonequilibrium Equality for Free Energy Differences.
Phys. Rev. Lett. 1997, 78 (14), 2690–2693.
DOI: 10.1103/PhysRevLett.78.2690
[Jarzynski-1997b]
Jarzynski, C.
Equilibrium Free-Energy Differences from Nonequilibrium Measurements: A Master-Equation Approach.
Phys. Rev. E 1997, 56 (5), 5018–5035.
DOI: 10.1103/physreve.56.5018
[Liu-2013]
Liu, S.; Wu, Y.; Lin, T.; Abel, R.; Redmann, J.P.; Summa, C.M.; Jaber, V.R.; Lim, N.M.; Mobley, D.L.
Lead Optimization Mapper: Automating Free Energy Calculations for Lead Optimization.
J. Comput.-Aided Mol. Des. 2013, 27 (9), 755–770.
DOI: 10.1007/s10822-013-9678-y
[PDB-IDs]
RCSB Protein Databank. https://www.rcsb.org/
Structures Followed by Corresponding Ligands:
PDB ID: 2C6I Citation: Richardson, C.M.; Williamson, D.S.; Parratt, M.J.; Borgognoni, J.; Cansfield, A.D.; Dokurno, P.; Francis, G.L.; Howes, R.; et al. Triazolo[1,5-a]pyrimidines as novel CDK2 inhibitors: Protein structure-guided design and SAR. (2018) DOI 10.1016/j.bmcl.2005.11.048
PDB ID: DT1 triazolopyrimidine inhibitor
PDB ID: 2BTS Citation: Vulpetti, A.; Casale, E.; Roletto, F.; Amici, R.; Villa, M.; Pevarello, P. Structure-Based Drug Design to the Discovery of New 2-Aminothiazole Cdk2 Inhibitors. (2006) DOI 10.1016/j.jmgm.2005.09.012
PDB ID: U32
PDB ID: 2CHM Citation: Allerton, C.M.N.; Barber, C.G.; Beaumont, K.C; Brown, D.G.; Cole, S.M.; Ellis, D.; Lane, C.A.L.; Maw, G.N.; et al. A Novel Series of Potent and Selective PDE5 Inhibitors with Potential for High and Dose-Independent Oral Bioavailability. (2006) DOI 10.1021/jm060113e
PDB ID: 3P4
PDB ID: 1XP0 Citation: Card, G.L.; England, B.P.; Suzuki, Y.; Fong, D.; Powell, B.; Lee, B.; Luu, C.; Tabrizizad, M.; et al. Structural Basis for the Activity of Drugs that Inhibit Phosphodiesterases. (2004) DOI 10.1016/j.str.2004.10.004
PDB ID: VDN
[Wang-2015]
Wang, Lingle and Wu, Yujie and Deng, Yuqing and Kim, Byungchan and Pierce, Levi and Krilov, Goran and Lupyan, Dmitry and Robinson, Shaughnessy and Dahlgren, Markus K. and Greenwood, Jeremy and Romero, Donna L. and Masse, Craig and Knight, Jennifer L. and Steinbrecher, Thomas and Beuming, Thijs and Damm, Wolfgang and Harder, Ed and Sherman, Woody and Brewer, Mark and Wester, Ron and Murcko, Mark and Frye, Leah and Farid, Ramy and Lin, Teng and Mobley, David L. and Jorgensen, William L. and Berne, Bruce J. and Friesner, Richard A. and Abel, Robert
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
J. Am. Chem. Soc., 2015, 137 (7), 2695-2703.
DOI: 10.1021/ja512751q
[Warren-2012]
Warren, G.L.; Do, T.D.; Kelley, B.P.; Nicholls, A.; Warren, S.D.
Essential Considerations for Using Protein–Ligand Structures in Drug Discovery.
Drug Discovery Today 2012, 17, 1270–1281.
DOI: 10.1016/j.drudis.2012.06.011
[Xu-2019]
Xu, H.
Optimal Measurement Network of Pairwise Differences.
J. Chem. Inf. Model. 2019, 59 (11), 4720–4728.
DOI: 10.1021/acs.jcim.9b00528