Challenges in Modelling Metalloenzymes
523
6. Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC,
Silakov A, Bollinger JM, Krebs C, Boal AK (2017) J Am Chem Soc 139:13830
7. Kovaleva EG, Lipscomb JD (2007) Science 316:453
8. Zheng H, Chordia MD, Cooper DR, Chruszcz M, Müller P, Sheldrick GM, Minor W (2013)
Nat Protoc 9:156
9. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017) Acta Crystallogr
Sect D Struct Biol 73:223
10. Fernández-Leiro R, Pereira-Rodríguez Á, Cerdán ME, Becerra M, Sanz-Aparicio J (2010) J
Biol Chem 285:28020
11. Ryde U, Nilsson K (2003) J Mol Struct THEOCHEM 632:259
12. Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539
13. Cao L, Caldararu O, Ryde U (2017) J Phys Chem B 121:8242
14. Ryde U(2007) Dalt Trans 607
15. Orry AJW, Abagyan R (eds) (2012) Homology modeling. Humana Press, Totowa, NJ
16. Webb B, Sali A (2016) Current protocols in bioinformatics. Wiley, Hoboken, NJ, USA, pp
5.6.1–5.6.37
17. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2014) Nat Methods 12:7
18. Bordoli L, Schwede, T (2011) Methods Mol Biol, 107–136
19. Kluza A, Niedzialkowska E, Kurpiewska K, Wojdyla Z, Quesne M, Kot E, Porebski PJ,
Borowski T (2018) J Struct Biol 202:229
20. Fiser A, Do RK, Sali A, Fiser A, Kinh R, Do G, Andrej S (2000) Protein Sci 9:1753
21. Lee J, Lee D, Park H, Coutsias EA, Seok C (2010) Proteins Struct Funct Bioinforma 78:3428
22. Tang K, Zhang J, Liang J (2014) PLoS Comput Biol 10:e1003539
23. Höppner A, Widderich N, Lenders M, Bremer E, Smits SHJ (2014) J Biol Chem 289:29570
24. Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E (2010) PLoS ONE 5:e10647
25. Melo F, Feytmans E (1998) J Mol Biol 277:1141
26. Sali A, Sali, A (2006) Protein Sci, 2507
27. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283
28. Widderich, N, Ho¨ ppner, A, Pittelkow M, Heider J, Smits SHJ, Bremer E (2014) PLoS One 9
29. Ullmann GM, Bombarda E (2014) Protein model. Springer, Cham, pp 135–163
30. Nielsen, JE (2008) In: Annual reports in computational chemistry. Elsevier, pp 89–106
31. Iwai W, Yagi D, Ishikawa T, Ohnishi Y, Tanaka I, Niimura N (2008) J Synchrotron Radiat
15:312
32. Moser A, Range K, York DM (2010) J Phys Chem B 114:13911
33. Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN (2006) Protein Sci 15:1214
34. Jensen JH, Li H, Robertson AD, Molina PA (2005) J Phys Chem A 109:6634
35. Awoonor-Williams E, Rowley CN (2016) J Chem Theory Comput 12:4662
36. Nielsen, JE, Gunner MR, García-Moreno BE (2011) Proteins Struct Funct Bioinforma 79:3249
37. Wasilewska M, Adamczyk Z, Jachimska B (2009) Langmuir 25:3698
38. Righetti PG (2004) J Chromatogr A 1037:491
39. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) J Chem Theory Comput
7:525
40. Spassov VZ, Yan L (2008) Protein Sci 17:1955
41. Kumosinski TF, Brown EM, Farrell HM (1994) In: Molecular modeling from virtual tools to
real problems, pp 368–390
42. Kumosinski TF, Brown EM, Farrell HM (1993) J Dairy Sci 76:931
43. Uranga J, Mikulskis P, Genheden S, Ryde U (2012) Comput. Theor Chem 1000:75
44. Szyk-Warszy´ nska L, Gergely C, Jarek E, Cuisinier F, Socha RP, Warszy´ nski P (2009) Colloids
Surf A Physicochem Eng Asp 343:118
45. Ui N (1971) Biochim Biophys Acta Protein Struct 229:582
46. Jachimska B, Wasilewska M, Adamczyk Z (2008) Langmuir 24:6866
47. Wasilewska M, Adamczyk Z (2011) Langmuir 27:686
48. Ullmann MG, Noodleman L, Case DA (2002) JBIC J Biol Inorg Chem 7:632
49. Bombarda E, Ullmann GM (2010) J Phys Chem B 114:1994
523
6. Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC,
Silakov A, Bollinger JM, Krebs C, Boal AK (2017) J Am Chem Soc 139:13830
7. Kovaleva EG, Lipscomb JD (2007) Science 316:453
8. Zheng H, Chordia MD, Cooper DR, Chruszcz M, Müller P, Sheldrick GM, Minor W (2013)
Nat Protoc 9:156
9. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017) Acta Crystallogr
Sect D Struct Biol 73:223
10. Fernández-Leiro R, Pereira-Rodríguez Á, Cerdán ME, Becerra M, Sanz-Aparicio J (2010) J
Biol Chem 285:28020
11. Ryde U, Nilsson K (2003) J Mol Struct THEOCHEM 632:259
12. Nilsson K, Ryde U (2004) J Inorg Biochem 98:1539
13. Cao L, Caldararu O, Ryde U (2017) J Phys Chem B 121:8242
14. Ryde U(2007) Dalt Trans 607
15. Orry AJW, Abagyan R (eds) (2012) Homology modeling. Humana Press, Totowa, NJ
16. Webb B, Sali A (2016) Current protocols in bioinformatics. Wiley, Hoboken, NJ, USA, pp
5.6.1–5.6.37
17. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y (2014) Nat Methods 12:7
18. Bordoli L, Schwede, T (2011) Methods Mol Biol, 107–136
19. Kluza A, Niedzialkowska E, Kurpiewska K, Wojdyla Z, Quesne M, Kot E, Porebski PJ,
Borowski T (2018) J Struct Biol 202:229
20. Fiser A, Do RK, Sali A, Fiser A, Kinh R, Do G, Andrej S (2000) Protein Sci 9:1753
21. Lee J, Lee D, Park H, Coutsias EA, Seok C (2010) Proteins Struct Funct Bioinforma 78:3428
22. Tang K, Zhang J, Liang J (2014) PLoS Comput Biol 10:e1003539
23. Höppner A, Widderich N, Lenders M, Bremer E, Smits SHJ (2014) J Biol Chem 289:29570
24. Reuter K, Pittelkow M, Bursy J, Heine A, Craan T, Bremer E (2010) PLoS ONE 5:e10647
25. Melo F, Feytmans E (1998) J Mol Biol 277:1141
26. Sali A, Sali, A (2006) Protein Sci, 2507
27. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283
28. Widderich, N, Ho¨ ppner, A, Pittelkow M, Heider J, Smits SHJ, Bremer E (2014) PLoS One 9
29. Ullmann GM, Bombarda E (2014) Protein model. Springer, Cham, pp 135–163
30. Nielsen, JE (2008) In: Annual reports in computational chemistry. Elsevier, pp 89–106
31. Iwai W, Yagi D, Ishikawa T, Ohnishi Y, Tanaka I, Niimura N (2008) J Synchrotron Radiat
15:312
32. Moser A, Range K, York DM (2010) J Phys Chem B 114:13911
33. Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN (2006) Protein Sci 15:1214
34. Jensen JH, Li H, Robertson AD, Molina PA (2005) J Phys Chem A 109:6634
35. Awoonor-Williams E, Rowley CN (2016) J Chem Theory Comput 12:4662
36. Nielsen, JE, Gunner MR, García-Moreno BE (2011) Proteins Struct Funct Bioinforma 79:3249
37. Wasilewska M, Adamczyk Z, Jachimska B (2009) Langmuir 25:3698
38. Righetti PG (2004) J Chromatogr A 1037:491
39. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) J Chem Theory Comput
7:525
40. Spassov VZ, Yan L (2008) Protein Sci 17:1955
41. Kumosinski TF, Brown EM, Farrell HM (1994) In: Molecular modeling from virtual tools to
real problems, pp 368–390
42. Kumosinski TF, Brown EM, Farrell HM (1993) J Dairy Sci 76:931
43. Uranga J, Mikulskis P, Genheden S, Ryde U (2012) Comput. Theor Chem 1000:75
44. Szyk-Warszy´ nska L, Gergely C, Jarek E, Cuisinier F, Socha RP, Warszy´ nski P (2009) Colloids
Surf A Physicochem Eng Asp 343:118
45. Ui N (1971) Biochim Biophys Acta Protein Struct 229:582
46. Jachimska B, Wasilewska M, Adamczyk Z (2008) Langmuir 24:6866
47. Wasilewska M, Adamczyk Z (2011) Langmuir 27:686
48. Ullmann MG, Noodleman L, Case DA (2002) JBIC J Biol Inorg Chem 7:632
49. Bombarda E, Ullmann GM (2010) J Phys Chem B 114:1994