29. Montgomery JA, Niwas S, Rose JD et al (1993) Structure-based design of inhibitors of
purine nucleoside phosphorylase. 1. 9-(arylmethyl) derivatives of 9-deazaguanine. J Med
Chem 36:55–69. https://doi.org/10.1021/jm00053a008
30. Ealick SE, Babu YS, Bugg CE et al (1993) Application of X-ray crystallographic methods in
the design of purine nucleoside phosphorylase inhibitors. Ann N Y Acad Sci 685:237–247
31. Ealick SE, Babu YS, Bugg CE et al (1991) Application of crystallographic and modeling
methods in the design of purine nucleoside phosphorylase inhibitors. Proc Natl Acad Sci U S
A 88:11540–11544. https://doi.org/10.1073/pnas.89.20.9974c
32. Erion MD, Niwas S, Rose JD et al (1993) Structure-based design of inhibitors of purine
nucleoside phosphorylase. 3. 9-arylmethyl derivatives of 9-deazaguanine substituted on the
arylmethyl group. J Med Chem 36:3771–3783. https://doi.org/10.1021/jm00076a004
33. Freire E (2008) Do enthalpy and entropy distinguish first in class from best in class? Drug
Discov Today 13:869–874. https://doi.org/10.1016/j.drudis.2008.07.005
34. Ho M-C, Shi W, Rinaldo-Matthis A et al (2010) Four generations of transition-state
analogues for human purine nucleoside phosphorylase. Proc Natl Acad Sci 107:4805–4812.
https://doi.org/10.1073/pnas.0913439107
35. Edwards AA, Mason JM, Clinch K et al (2009) Altered enthalpy-entropy compensation in
picomolar transition state analogues of human purine nucleoside phosphorylase.
Biochemistry 48:5226–5238. https://doi.org/10.1021/bi9005896
36. Ohtaka H, Freire E (2005) Adaptive inhibitors of the HIV-1 protease. Prog Biophys Mol
Biol 88:193–208. https://doi.org/10.1016/j.pbiomolbio.2004.07.005
37. Muzammil S, Armstrong AA, Kang LW et al (2007) Unique thermodynamic response of
tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.
J Virol 81:5144–5154. https://doi.org/10.1128/jvi.02706-06
38. Carbonell T, Freire E (2005) Binding thermodynamics of statins to HMG-CoA reductase.
Biochemistry 44:11741–11748. https://doi.org/10.1021/bi050905v
39. Du X, Li Y, Xia Y-L et al (2016) Insights into protein-ligand interactions: mechanisms,
models, and methods. Int J Mol Sci 17:144. https://doi.org/10.3390/ijms17020144
40. Amaral M., Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P,
Sirrenberg C, Wade RC, Frech M (2017) Protein conformational flexibility modulates
kinetics and thermodynamics of drug binding. Nat Commun. https://doi.org/10.1038/
s41467-017-02258-w
41. De Sanctis V, Kattamis C, Canatan D et al (2017) b-thalassemia distribution in the old
world: an ancient disease seen from a historical standpoint. Mediterr J Hematol Infect Dis
9:1–14. https://doi.org/10.4084/mjhid.2017.018
42. Goss C, Giardina P, Degtyaryova D et al (2014) Red blood cell transfusions for thalassemia:
results of a survey assessing current practice and proposal of evidence-based guidelines.
Transfusion 54:1773–1781. https://doi.org/10.1111/trf.12571
43. Michlitsch J, Walters M (2008) Recent advances in bone marrow transplantation in
hemoglobinopathies. Curr Mol Med 8:675–689. https://doi.org/10.2174/156652408786241393
44. Human Hemoglobin Structures (PDB) (2018) http://www.rcsb.org/pdb/results/results.do?
tabtoshow=Current&qrid=205B68A9. Accessed 15 Feb 2018
45. Brown EN, Ramaswamy S (2007) Quality of protein crystal structures. Acta Crystallogr D
Biol Crystallogr 63:941–950. https://doi.org/10.1107/s0907444907033847
46. Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for
non-crystallographers, or how to get the best (but not more) from published macromolecular
structures. FEBS J 275:1–21. https://doi.org/10.1111/j.1742-4658.2007.06178.x
47. Muller P (2009) Practical suggestions for better crystal structures. Crystallogr Rev 15:57–83.
https://doi.org/10.1080/08893110802547240
48. Deller MC, Rupp B (2015) Models of protein-ligand crystal structures: trust, but verify.
J Comput Aided Mol Des 29:817–836. https://doi.org/10.1007/s10822-015-9833-8
49. Carugo O (2018) How large B-factors can be in protein crystal structures. BMC Bioinform
19:1–9. https://doi.org/10.1186/s12859-018-2083-8
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
163
purine nucleoside phosphorylase. 1. 9-(arylmethyl) derivatives of 9-deazaguanine. J Med
Chem 36:55–69. https://doi.org/10.1021/jm00053a008
30. Ealick SE, Babu YS, Bugg CE et al (1993) Application of X-ray crystallographic methods in
the design of purine nucleoside phosphorylase inhibitors. Ann N Y Acad Sci 685:237–247
31. Ealick SE, Babu YS, Bugg CE et al (1991) Application of crystallographic and modeling
methods in the design of purine nucleoside phosphorylase inhibitors. Proc Natl Acad Sci U S
A 88:11540–11544. https://doi.org/10.1073/pnas.89.20.9974c
32. Erion MD, Niwas S, Rose JD et al (1993) Structure-based design of inhibitors of purine
nucleoside phosphorylase. 3. 9-arylmethyl derivatives of 9-deazaguanine substituted on the
arylmethyl group. J Med Chem 36:3771–3783. https://doi.org/10.1021/jm00076a004
33. Freire E (2008) Do enthalpy and entropy distinguish first in class from best in class? Drug
Discov Today 13:869–874. https://doi.org/10.1016/j.drudis.2008.07.005
34. Ho M-C, Shi W, Rinaldo-Matthis A et al (2010) Four generations of transition-state
analogues for human purine nucleoside phosphorylase. Proc Natl Acad Sci 107:4805–4812.
https://doi.org/10.1073/pnas.0913439107
35. Edwards AA, Mason JM, Clinch K et al (2009) Altered enthalpy-entropy compensation in
picomolar transition state analogues of human purine nucleoside phosphorylase.
Biochemistry 48:5226–5238. https://doi.org/10.1021/bi9005896
36. Ohtaka H, Freire E (2005) Adaptive inhibitors of the HIV-1 protease. Prog Biophys Mol
Biol 88:193–208. https://doi.org/10.1016/j.pbiomolbio.2004.07.005
37. Muzammil S, Armstrong AA, Kang LW et al (2007) Unique thermodynamic response of
tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.
J Virol 81:5144–5154. https://doi.org/10.1128/jvi.02706-06
38. Carbonell T, Freire E (2005) Binding thermodynamics of statins to HMG-CoA reductase.
Biochemistry 44:11741–11748. https://doi.org/10.1021/bi050905v
39. Du X, Li Y, Xia Y-L et al (2016) Insights into protein-ligand interactions: mechanisms,
models, and methods. Int J Mol Sci 17:144. https://doi.org/10.3390/ijms17020144
40. Amaral M., Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P,
Sirrenberg C, Wade RC, Frech M (2017) Protein conformational flexibility modulates
kinetics and thermodynamics of drug binding. Nat Commun. https://doi.org/10.1038/
s41467-017-02258-w
41. De Sanctis V, Kattamis C, Canatan D et al (2017) b-thalassemia distribution in the old
world: an ancient disease seen from a historical standpoint. Mediterr J Hematol Infect Dis
9:1–14. https://doi.org/10.4084/mjhid.2017.018
42. Goss C, Giardina P, Degtyaryova D et al (2014) Red blood cell transfusions for thalassemia:
results of a survey assessing current practice and proposal of evidence-based guidelines.
Transfusion 54:1773–1781. https://doi.org/10.1111/trf.12571
43. Michlitsch J, Walters M (2008) Recent advances in bone marrow transplantation in
hemoglobinopathies. Curr Mol Med 8:675–689. https://doi.org/10.2174/156652408786241393
44. Human Hemoglobin Structures (PDB) (2018) http://www.rcsb.org/pdb/results/results.do?
tabtoshow=Current&qrid=205B68A9. Accessed 15 Feb 2018
45. Brown EN, Ramaswamy S (2007) Quality of protein crystal structures. Acta Crystallogr D
Biol Crystallogr 63:941–950. https://doi.org/10.1107/s0907444907033847
46. Wlodawer A, Minor W, Dauter Z, Jaskolski M (2008) Protein crystallography for
non-crystallographers, or how to get the best (but not more) from published macromolecular
structures. FEBS J 275:1–21. https://doi.org/10.1111/j.1742-4658.2007.06178.x
47. Muller P (2009) Practical suggestions for better crystal structures. Crystallogr Rev 15:57–83.
https://doi.org/10.1080/08893110802547240
48. Deller MC, Rupp B (2015) Models of protein-ligand crystal structures: trust, but verify.
J Comput Aided Mol Des 29:817–836. https://doi.org/10.1007/s10822-015-9833-8
49. Carugo O (2018) How large B-factors can be in protein crystal structures. BMC Bioinform
19:1–9. https://doi.org/10.1186/s12859-018-2083-8
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
163