4. Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M,
Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS
(2006) A critical assessment of docking programs and scoring functions. J Med Chem 49
(20):5912–5931. https://doi.org/10.1021/jm050362n
5. Gilson MK, Zhou HX (2007) Calculation of protein-ligand binding affinities. Annu Rev
Biophys Biomol Struct 36:21–42. https://doi.org/10.1146/annurev.biophys.36.040306.
132550
6. Armen RS, Chen J, Brooks 3rd CL (2009) An evaluation of explicit receptor flexibility in
molecular docking using molecular dynamics and torsion angle molecular dynamics. J Chem
Theory Comput 5(10):2909–2923. https://doi.org/10.1021/ct900262t
7. Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery.
BMC Biol 9:71. https://doi.org/10.1186/1741-7007-9-71
8. Wichapong K, Rohe A, Platzer C, Slynko I, Erdmann F, Schmidt M, Sippl W (2014)
Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase
inhibitors. J Chem Inf Model 54(3):881–893. https://doi.org/10.1021/ci4007326
9. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent
studies of the stability of DNA, RNA, and phosphoramidateÀDNA helices. J Am Chem Soc
120(37):9401–9409. https://doi.org/10.1021/ja981844+
10. Abel R, Wang L, Mobley DL, Friesner RA (2017) A critical review of validation, blind testing,
and real-world use of alchemical protein-ligand binding free energy calculations. Curr Top
Med Chem 17(23):2577–2585. https://doi.org/10.2174/1568026617666170414142131
11. Kaus JW, McCammon JA (2015) Enhanced ligand sampling for relative protein-ligand
binding free energy calculations. J Phys Chem B 119(20):6190–6197. https://doi.org/10.
1021/acs.jpcb.5b02348
12. Klimovich PV, Shirts MR, Mobley DL (2015) Guidelines for the analysis of free energy
calculations. J Comput Aided Mol Des 29(5):397–411. https://doi.org/10.1007/s10822-0159840-9
13. Deng N, Flynn WF, Xia J, Vijayan RSK, Zhang B, He P, Mentes A, Gallicchio E, Levy RM
(2016) Large scale free energy calculations for blind predictions of protein–ligand binding: the
D3R Grand Challenge 2015. J Comput Aided Mol Des 30(9):743–751. https://doi.org/10.
1007/s10822-016-9952-x
14. Lindström A, Edvinsson L, Johansson A, Andersson CD, Andersson IE, Raubacher F,
Linusson A (2011) Postprocessing of docked proteinÀligand complexes using implicit solvation models. J Chem Inf Model 51(2):267–282. https://doi.org/10.1021/ci100354x
15. Daniel C, Woody S, Thijs B (2017) Calculating water thermodynamics in the binding site of
proteins – applications of watermap to drug discovery. Curr Top Med Chem 17
(23):2586–2598. https://doi.org/10.2174/1568026617666170414141452
16. de Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB (2003) Histone
deacetylases (HDACs): characterization of the classical HDAC family. Biochem J 370
(Pt 3):737–749. https://doi.org/10.1042/BJ20021321
17. Hodawadekar SC, Marmorstein R (2007) Chemistry of acetyl transfer by histone modifying
enzymes: structure, mechanism and implications for effector design. Oncogene 26
(37):5528–5540. https://doi.org/10.1038/sj.onc.1210619
18. Somoza JR, Skene RJ, Katz BA, Mol C, Ho JD, Jennings AJ, Luong C, Arvai A, Buggy JJ,
Chi E, Tang J, Sang BC, Verner E, Wynands R, Leahy EM, Dougan DR, Snell G, Navre M,
Knuth MW, Swanson RV, McRee DE, Tari LW (2004) Structural snapshots of human
HDAC8 provide insights into the class I histone deacetylases. Structure 12(7):1325–1334.
https://doi.org/10.1016/j.str.2004.04.012
19. Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P,
Neddermann P, De Francesco R, Steinkuhler C, Gallinari P, Carfi A (2008) Structural and
functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zincbinding domain. J Biol Chem 283(39):26694–26704. https://doi.org/10.1074/jbc.M803514200
20. Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R,
Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN,
476
D. Robaa et al.
Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS
(2006) A critical assessment of docking programs and scoring functions. J Med Chem 49
(20):5912–5931. https://doi.org/10.1021/jm050362n
5. Gilson MK, Zhou HX (2007) Calculation of protein-ligand binding affinities. Annu Rev
Biophys Biomol Struct 36:21–42. https://doi.org/10.1146/annurev.biophys.36.040306.
132550
6. Armen RS, Chen J, Brooks 3rd CL (2009) An evaluation of explicit receptor flexibility in
molecular docking using molecular dynamics and torsion angle molecular dynamics. J Chem
Theory Comput 5(10):2909–2923. https://doi.org/10.1021/ct900262t
7. Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery.
BMC Biol 9:71. https://doi.org/10.1186/1741-7007-9-71
8. Wichapong K, Rohe A, Platzer C, Slynko I, Erdmann F, Schmidt M, Sippl W (2014)
Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase
inhibitors. J Chem Inf Model 54(3):881–893. https://doi.org/10.1021/ci4007326
9. Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA (1998) Continuum solvent
studies of the stability of DNA, RNA, and phosphoramidateÀDNA helices. J Am Chem Soc
120(37):9401–9409. https://doi.org/10.1021/ja981844+
10. Abel R, Wang L, Mobley DL, Friesner RA (2017) A critical review of validation, blind testing,
and real-world use of alchemical protein-ligand binding free energy calculations. Curr Top
Med Chem 17(23):2577–2585. https://doi.org/10.2174/1568026617666170414142131
11. Kaus JW, McCammon JA (2015) Enhanced ligand sampling for relative protein-ligand
binding free energy calculations. J Phys Chem B 119(20):6190–6197. https://doi.org/10.
1021/acs.jpcb.5b02348
12. Klimovich PV, Shirts MR, Mobley DL (2015) Guidelines for the analysis of free energy
calculations. J Comput Aided Mol Des 29(5):397–411. https://doi.org/10.1007/s10822-0159840-9
13. Deng N, Flynn WF, Xia J, Vijayan RSK, Zhang B, He P, Mentes A, Gallicchio E, Levy RM
(2016) Large scale free energy calculations for blind predictions of protein–ligand binding: the
D3R Grand Challenge 2015. J Comput Aided Mol Des 30(9):743–751. https://doi.org/10.
1007/s10822-016-9952-x
14. Lindström A, Edvinsson L, Johansson A, Andersson CD, Andersson IE, Raubacher F,
Linusson A (2011) Postprocessing of docked proteinÀligand complexes using implicit solvation models. J Chem Inf Model 51(2):267–282. https://doi.org/10.1021/ci100354x
15. Daniel C, Woody S, Thijs B (2017) Calculating water thermodynamics in the binding site of
proteins – applications of watermap to drug discovery. Curr Top Med Chem 17
(23):2586–2598. https://doi.org/10.2174/1568026617666170414141452
16. de Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB (2003) Histone
deacetylases (HDACs): characterization of the classical HDAC family. Biochem J 370
(Pt 3):737–749. https://doi.org/10.1042/BJ20021321
17. Hodawadekar SC, Marmorstein R (2007) Chemistry of acetyl transfer by histone modifying
enzymes: structure, mechanism and implications for effector design. Oncogene 26
(37):5528–5540. https://doi.org/10.1038/sj.onc.1210619
18. Somoza JR, Skene RJ, Katz BA, Mol C, Ho JD, Jennings AJ, Luong C, Arvai A, Buggy JJ,
Chi E, Tang J, Sang BC, Verner E, Wynands R, Leahy EM, Dougan DR, Snell G, Navre M,
Knuth MW, Swanson RV, McRee DE, Tari LW (2004) Structural snapshots of human
HDAC8 provide insights into the class I histone deacetylases. Structure 12(7):1325–1334.
https://doi.org/10.1016/j.str.2004.04.012
19. Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P,
Neddermann P, De Francesco R, Steinkuhler C, Gallinari P, Carfi A (2008) Structural and
functional analysis of the human HDAC4 catalytic domain reveals a regulatory structural zincbinding domain. J Biol Chem 283(39):26694–26704. https://doi.org/10.1074/jbc.M803514200
20. Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R,
Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN,
476
D. Robaa et al.