SCOPUS 정보 검색 플랫폼

Journal of Computational Chemistry

Volumn 34, Issue 9, 2013, Pages 750-756

The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics †

(5) Nowosielski, Marcin a Hoffmann, Marcin b Kuron, Aneta a Korycka Machala, Malgorzata a Dziadek, Jaroslaw a

a INSTITUTE OF MEDICAL BIOLOGY (Poland)

b ADAM MICKIEWICZ UNIVERSITY (Poland)

Author keywords

docking; drug design; molecular mechanics; quantum mechanics; tuberculosis

Indexed keywords

BINDING ENERGY; DOCKING; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROTEINS; QUANTUM THEORY; SULFUR COMPOUNDS;

BINDING AFFINITIES; DRUG DESIGN; MYCOBACTERIUM TUBERCULOSIS; PROTEIN FLEXIBILITY; PROTEIN-LIGAND INTERACTIONS; QUANTUM MECHANICAL; ROOT MEAN SQUARE DEVIATIONS; TUBERCULOSIS;

MECHANICS;

EID: 84874646837 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.23192 Document Type: Article

Times cited : (11)

References (50)

1
- 33748276474
- S. F. Sousa, P. A. Fernandes, M. J. Ramos, Proteins 2006, 65, 15.
- (2006) Proteins , vol.65 , pp. 15
- Sousa, S.F.¹ Fernandes, P.A.² Ramos, M.J.³

2
- 79960224972
- S. L. Kinnings, N. N. Liu, P. J. Tonge, R. M. Jackson, L. Xie, P. E. Bourne, J. Chem. Inf. Model. 2011, 51, 1195.
- (2011) J. Chem. Inf. Model. , vol.51 , pp. 1195
- Kinnings, S.L.¹ Liu, N.N.² Tonge, P.J.³ Jackson, R.M.⁴ Xie, L.⁵ Bourne, P.E.⁶

3
- 78149495244
- J. D. Durrant, J. A. McCammon, Curr. Opin. Pharmacol. 2010, 10, 770.
- (2010) Curr. Opin. Pharmacol. , vol.10 , pp. 770
- Durrant, J.D.¹ McCammon, J.A.²

4
- 57449089629
- Ch. J. R. Illingworth, G. M. Morris, K. E. B. Parkes, Ch. R. Snell, Ch. A. Reynolds, J. Phys. Chem. A 2008, 112, 12157.
- (2008) J. Phys. Chem. A , vol.112 , pp. 12157
- Illingworth, Ch.J.R.¹ Morris, G.M.² Parkes, K.E.B.³ Snell, Ch.R.⁴ Reynolds, Ch.A.⁵

5
- 79251524915
- D. Plewczynski, M. Łaźniewski, R. Augustyniak, K. Ginalski, J. Comput. Chem. 2011, 32, 742.
- (2011) J. Comput. Chem. , vol.32 , pp. 742
- Plewczynski, D.¹ Łaźniewski, M.² Augustyniak, R.³ Ginalski, K.⁴

6
- 33747200808
- H. Alonso, A. A. Bliznyuk, J. E. Gready, Med. Res. Rev. 2006, 26, 531.
- (2006) Med. Res. Rev. , vol.26 , pp. 531
- Alonso, H.¹ Bliznyuk, A.A.² Gready, J.E.³

7
- 77949345617
- T. Zhou, D. Huang, A. Caflish, Curr. Top. Med. Chem. 2010, 10, 33.
- (2010) Curr. Top. Med. Chem. , vol.10 , pp. 33
- Zhou, T.¹ Huang, D.² Caflish, A.³

8
- 23944459025
- A. Khandelwal, V. Lukacova, D. Comez, D. M. Kroll, S. Raha, A. Balaz, J. Med. Chem. 2005, 48, 5437.
- (2005) J. Med. Chem. , vol.48 , pp. 5437
- Khandelwal, A.¹ Lukacova, V.² Comez, D.³ Kroll, D.M.⁴ Raha, S.⁵ Balaz, A.⁶

9
- 79952141712
- M. Nowosielski, M. Hoffmann, L. S. Wyrwicz, P. Stepniak, D. M. Plewczynski, M. Lazniewski, K. Ginalski, L. Rychlewski, J. Chem. Inf. Model. 2011, 51, 455.
- (2011) J. Chem. Inf. Model. , vol.51 , pp. 455
- Nowosielski, M.¹ Hoffmann, M.² Wyrwicz, L.S.³ Stepniak, P.⁴ Plewczynski, D.M.⁵ Lazniewski, M.⁶ Ginalski, K.⁷ Rychlewski, L.⁸

10
- 59449099151
- A. Ciulli, D. E. Scott, M. Ando, F. Reyes, S. A. Saldanha, K. L. Tuck, D. Y. Chirgadze, T. L. Blundell, Ch. Abell, ChemBioChem 2008, 9, 2606.
- (2008) ChemBioChem , vol.9 , pp. 2606
- Ciulli, A.¹ Scott, D.E.² Ando, M.³ Reyes, F.⁴ Saldanha, S.A.⁵ Tuck, K.L.⁶ Chirgadze, D.Y.⁷ Blundell, T.L.⁸ Abell, Ch.⁹

11
- 84874645853
- Global tuberculosis control: WHO report (Accessed November 30, 2012)
- Global tuberculosis control: WHO report, 2010. http://www.who.int/tb/ features-;archive/gtbr10summary.pdf (Accessed November 30, 2012)
- (2010)

12
- 58149109426
- H. Eoh, P. J. Brennan, D. C. Crick, Tuberculosis 2009, 89, 1.
- (2009) Tuberculosis , vol.89 , pp. 1
- Eoh, H.¹ Brennan, P.J.² Crick, D.C.³

13
- 33745607880
- S. Hasan, S. Daugelat, P. S. S. Rao, M. Schreiber, PLOS Comput. Biol. 2006, 2, 0539.
- (2006) PLOS Comput. Biol. , vol.2 , pp. 0539
- Hasan, S.¹ Daugelat, S.² Rao, P.S.S.³ Schreiber, M.⁴

14
- 27644588079
- S. Anishetty, M. Pulimi, G. Pennathur, Comput. Biol. Chem. 2005, 29, 368.
- (2005) Comput. Biol. Chem. , vol.29 , pp. 368
- Anishetty, S.¹ Pulimi, M.² Pennathur, G.³

15
- 62449223765
- K. Raman, K. Yeturu, N. Chandra, BMC Syst. Biol. 2008, 2, 109.
- (2008) BMC Syst. Biol. , vol.2 , pp. 109
- Raman, K.¹ Yeturu, K.² Chandra, N.³

16
- 34547637078
- M. Korycka-Machala, E. Rychta, A. Brzostek, H. R. Sayer, A. Rumijowska-Galewicz, R. P. Bowater, J. Dziadek, Antimicrob. Agents Chemother. 2007, 51, 2888.
- (2007) Antimicrob. Agents Chemother. , vol.51 , pp. 2888
- Korycka-Machala, M.¹ Rychta, E.² Brzostek, A.³ Sayer, H.R.⁴ Rumijowska-Galewicz, A.⁵ Bowater, R.P.⁶ Dziadek, J.⁷

17
- 45249093620
- N. Dwivedi, D. Dube, J. Pandey, B. Singh, V. Kukshal, R. Ramachandran, R. P. Tripathi, Med. Res. Rev. 2008, 28, 545.
- (2008) Med. Res. Rev. , vol.28 , pp. 545
- Dwivedi, N.¹ Dube, D.² Pandey, J.³ Singh, B.⁴ Kukshal, V.⁵ Ramachandran, R.⁶ Tripathi, R.P.⁷

18
- 33748419613
- K. Mdluli, M. Spigelman, Curr. Opin. Pharmacol. 2006, 6, 459.
- (2006) Curr. Opin. Pharmacol. , vol.6 , pp. 459
- Mdluli, K.¹ Spigelman, M.²

19
- 33846874537
- E. L. White, K. Southworth, L. Ross, S. Cooley, R. B. Gill, M. I. Sosa, A. Manouvakhova, L. Rasmussen, C. Goulding, D. Eisenberg, T. M. Fletcher, III, J. Biomol. Screen. 2007, 12, 100.
- (2007) J. Biomol. Screen. , vol.12 , pp. 100
- White, E.L.¹ Southworth, K.² Ross, L.³ Cooley, S.⁴ Gill, R.B.⁵ Sosa, M.I.⁶ Manouvakhova, A.⁷ Rasmussen, L.⁸ Goulding, C.⁹ Eisenberg, D.¹⁰ Fletcher III, T.M.¹¹

20
- 79958708761
- Y. Yang, P. Gao, Y. Liu, X. Ji, M. Gan, Y. Guan, X. Hao, Z. Li, C. Xiao, Bioorg. Med. Chem. Lett. 2011, 21, 3943.
- (2011) Bioorg. Med. Chem. Lett. , vol.21 , pp. 3943
- Yang, Y.¹ Gao, P.² Liu, Y.³ Ji, X.⁴ Gan, M.⁵ Guan, Y.⁶ Hao, X.⁷ Li, Z.⁸ Xiao, C.⁹

21
- 0036796061
- V. K. Sambandamurthy, X. Wang, B. Chen, R. G. Russell, S. Derrick, F. M. Collins, S. L. Morris, W. R. Jacobs, Nat. Med. 2002, 8, 1171.
- (2002) Nat. Med. , vol.8 , pp. 1171
- Sambandamurthy, V.K.¹ Wang, X.² Chen, B.³ Russell, R.G.⁴ Derrick, S.⁵ Collins, F.M.⁶ Morris, S.L.⁷ Jacobs, W.R.⁸

22
- 84874644955
- Qt 2008-2011 Nokia Corporation
- Qt 2008-2011 Nokia Corporation.

24
- 84890021933
- S. F. Boys, F. Bernardi, Mol. Phys. 1970, 19, 553.
- (1970) Mol. Phys. , vol.19 , pp. 553
- Boys, S.F.¹ Bernardi, F.²

25
- 84986513567
- C. M. Breneman, K. B. Wiberg, J. Comput. Chem. 1990, 11, 361.
- (1990) J. Comput. Chem. , vol.11 , pp. 361
- Breneman, C.M.¹ Wiberg, K.B.²

26
- 27344436659
- J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
- (2005) J. Comput. Chem. , vol.26 , pp. 1781
- Phillips, J.C.¹ Braun, R.² Wang, W.³ Gumbart, J.⁴ Tajkhorshid, E.⁵ Villa, E.⁶ Chipot, C.⁷ Skeel, R.D.⁸ Kalé, L.⁹ Schulten, K.¹⁰

27
- 0041784950
- A. D. MacKerell Jr., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586.
- (1998) J. Phys. Chem. B , vol.102 , pp. 3586
- MacKerell, Jr.A.D.¹ Bashford, D.² Bellott, M.³ Dunbrack, Jr.R.L.⁴ Evanseck, J.D.⁵ Field, M.J.⁶ Fischer, S.⁷ Gao, J.⁸ Guo, H.⁹ Ha, S.¹⁰ Joseph-Mccarthy, D.¹¹ Kuchnir, L.¹² Kuczera, K.¹³ Lau, F.T.K.¹⁴ Mattos, C.¹⁵ Michnick, S.¹⁶ Ngo, T.¹⁷ Nguyen, D.T.¹⁸ Prodhom, B.¹⁹ Reiher III, W.E.²⁰ more..

28
- 76249087938
- K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. MacKerell, Jr., J. Comput. Chem. 2010, 31, 671.
- (2010) J. Comput. Chem. , vol.31 , pp. 671
- Vanommeslaeghe, K.¹ Hatcher, E.² Acharya, C.³ Kundu, S.⁴ Zhong, S.⁵ Shim, J.⁶ Darian, E.⁷ Guvench, O.⁸ Lopes, P.⁹ Vorobyov, I.¹⁰ MacKerell, Jr.A.D.¹¹

29
- 84874659874
- accessed November 20
- www.ParamChem.org (accessed November 20, 2011).
- (2011)

30
- 11644261806
- G. M. Morris, D. S. Goodsell, R. S. Halliday, R. Huey, W. E. Hart, R. K. Belew, A. J. Olsen, J. Comput. Chem. 1998, 19, 1639
- (1998) J. Comput. Chem. , vol.19 , pp. 1639
- Morris, G.M.¹ Goodsell, D.S.² Halliday, R.S.³ Huey, R.⁴ Hart, W.E.⁵ Belew, R.K.⁶ Olsen, A.J.⁷

31
- 0029878720
- W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 1996, 14, 33.
- (1996) J. Mol. Graph. , vol.14 , pp. 33
- Humphrey, W.¹ Dalke, A.² Schulten, K.³

32
- 4444221565
- E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, T. E. Ferrin, J. Comput. Chem. 2004, 25, 1605.
- (2004) J. Comput. Chem. , vol.25 , pp. 1605
- Pettersen, E.F.¹ Goddard, T.D.² Huang, C.C.³ Couch, G.S.⁴ Greenblatt, D.M.⁵ Meng, E.C.⁶ Ferrin, T.E.⁷

33
- 0017411710
- F. C. Bernstein, T. F. Koetzle, G. J. Williams, E. E. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, M. Tasumi, J. Mol. Biol. 1977, 112, 535.
- (1977) J. Mol. Biol. , vol.112 , pp. 535
- Bernstein, F.C.¹ Koetzle, T.F.² Williams, G.J.³ Meyer, Jr.E.E.⁴ Brice, M.D.⁵ Rodgers, J.R.⁶ Kennard, O.⁷ Shimanouchi, T.⁸ Tasumi, M.⁹

34
- 0000937122
- P. Langevin, C. R. Acad. Sci. 1908, 146, 530.
- (1908) C. R. Acad. Sci. , vol.146 , pp. 530
- Langevin, P.¹

35
- 34250928962
- M. Born, Z. Phys. 1920, 1, 45.
- (1920) Z. Phys. , vol.1 , pp. 45
- Born, M.¹

36
- 0344778061
- W. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am. Chem. Soc. 1990, 112, 6127.
- (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127
- Still, W.C.¹ Tempczyk, A.² Hawley, R.C.³ Hendrickson, T.⁴

37
- 20644449471
- A. Onufriev, D. Bashford, D. A. Case, J.Phys. Chem. 2000, 104, 3712.
- (2000) J.Phys. Chem. , vol.104 , pp. 3712
- Onufriev, A.¹ Bashford, D.² Case, D.A.³

38
- 0004016501
- W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, J. Chem. Phys. 1983, 79, 926.
- (1983) J. Chem. Phys. , vol.79 , pp. 926
- Jorgensen, W.L.¹ Chandrasekhar, J.² Madura, J.D.³ Impey, R.W.⁴ Klein, M.L.⁵

39
- 33750587438
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684.
- (1984) J. Chem. Phys. , vol.81 , pp. 3684
- Berendsen, H.J.C.¹ Postma, J.P.M.² Van Gunsteren, W.F.³ Dinola, A.⁴ Haak, J.R.⁵

40
- 34547809547
- S. Nose, J. Chem. Phys. 1984, 81, 511.
- (1984) J. Chem. Phys. , vol.81 , pp. 511
- Nose, S.¹

41
- 0001538909
- W. G. Hoover, Phys. Rev. A 1985, 31, 1695.
- (1985) Phys. Rev. A , vol.31 , pp. 1695
- Hoover, W.G.¹

42
- 33846823909
- T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089.
- (1993) J. Chem. Phys. , vol.98 , pp. 10089
- Darden, T.¹ York, D.² Pedersen, L.³

43
- 43049141516
- Y. Zhao, D. G. Truhlar, Theor. Chem. Acc. 2008, 120, 215.
- (2008) Theor. Chem. Acc. , vol.120 , pp. 215
- Zhao, Y.¹ Truhlar, D.G.²

44
- 0037159941
- F. Jensen, J. Chem. Phys. 2002, 117, 9234.
- (2002) J. Chem. Phys. , vol.117 , pp. 9234
- Jensen, F.¹

45
- 0030059225
- H. Grubmuller, B. Heymann, P. Tavan, Science 1996, 271, 997.
- (1996) Science , vol.271 , pp. 997
- Grubmuller, H.¹ Heymann, B.² Tavan, P.³

46
- 7044239742
- P. Kollman, Chem. Rev. 1993, 93, 2395.
- (1993) Chem. Rev. , vol.93 , pp. 2395
- Kollman, P.¹

47
- 25044455217
- M. Head-Gordon, J. A. Pople, M. J. Frisch, Chem. Phys. Lett. 1988, 153, 503.
- (1988) Chem. Phys. Lett. , vol.153 , pp. 503
- Head-Gordon, M.¹ Pople, J.A.² Frisch, M.J.³

48
- 5444263418
- R. F. Fischetti, D. J. Rodi, D. B. Gore, L. Makowski, Chem. Biol. 2004, 11, 1431.
- (2004) Chem. Biol. , vol.11 , pp. 1431
- Fischetti, R.F.¹ Rodi, D.J.² Gore, D.B.³ Makowski, L.⁴

49
- 84874659457
- Paratool Plugin accessed November 20
- Paratool Plugin, http://www.ks.uiuc.edu/Research/vmd/plugins/paratool (accessed November 20, 2011).
- (2011)

50
- 33748538349
- J. Wang, W. Wang, P. A. Kollman, D. A. Case, J. Mol. Graph. Modell. 2006, 25, 247.
- (2006) J. Mol. Graph. Modell. , vol.25 , pp. 247
- Wang, J.¹ Wang, W.² Kollman, P.A.³ Case, D.A.⁴

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