SCOPUS 정보 검색 플랫폼

Volumn 35, Issue 14, 2014, Pages 1101-1105

ALMOST: An all atom molecular simulation toolkit for protein structure determination

(8) Fu, Biao a Sahakyan, Aleksandr B a Camilloni, Carlo a Tartaglia, Gian Gaetano b Paci, Emanuele c Caflisch, Amedeo d Vendruscolo, Michele a Cavalli, Andrea a,e

a UNIVERSITY OF CAMBRIDGE (United Kingdom)

b UNIVERSITAT POMPEU FABRA (Spain)

c UNIVERSITY OF LEEDS (United Kingdom)

d UNIVERSITY OF ZURICH (Switzerland)

e INSTITUTE FOR RESEARCH IN BIOMEDICINE (Switzerland)

Author keywords

chemical shifts; CHESHIRE; molecular dynamics; Molecular simulations; NMR spectroscopy; residual dipolar couplings

Indexed keywords

CHEMICAL SHIFT; COMPUTER OPERATING SYSTEMS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACIDS; OPEN SYSTEMS; PROTEINS;

CHESHIRE; COMPLEX MOLECULAR SYSTEMS; COMPUTATIONAL PACKAGE; MOLECULAR SIMULATIONS; NUCLEAR OVERHAUSER EFFECTS; RESIDUAL DIPOLAR COUPLINGS; STRUCTURAL RESTRAINTS; STRUCTURE DETERMINATION;

MOLECULAR STRUCTURE;

PROTEIN;

CHEMISTRY; COMPUTER PROGRAM; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN CONFORMATION;

MOLECULAR DYNAMICS SIMULATION; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 84899415888 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.23588 Document Type: Article

Times cited : (29)

References (39)

1
- 0003880161
- Garland Publications, New York
- B. Alberts, Molecular Biology of the Cell; Garland Publications, New York, 2008.
- (2008) Molecular Biology of the Cell
- Alberts, B.¹

2
- 0003818541
- Macmillan
- A. Fersht, Structure and Mechanism in Protein Science; Macmillan, 1999.
- (1999) Structure and Mechanism in Protein Science
- Fersht, A.¹

3
- 84863011912
- A. Rosato, J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Güntert, Y. He, T. Herrmann, Y. J. Huang, V. Jaravine, H. R. A. Jonker, M. A. Kennedy, O. F. Lange, G. Liu, T. E. Malliavin, R. Mani, B. Mao, G. T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T. A. Szyperski, M. Vendruscolo, R. Vernon, W. F. Vranken, S. de Vries, G. W. Vuister, B. Wu, Y. Yang, A. M. J. J. Bonvin, Structure 2012, 20, 227.
- (2012) Structure , vol.20 , pp. 227
- Rosato, A.¹ Aramini, J.M.² Arrowsmith, C.³ Bagaria, A.⁴ Baker, D.⁵ Cavalli, A.⁶ Doreleijers, J.F.⁷ Eletsky, A.⁸ Giachetti, A.⁹ Guerry, P.¹⁰ Gutmanas, A.¹¹ Güntert, P.¹² He, Y.¹³ Herrmann, T.¹⁴ Huang, Y.J.¹⁵ Jaravine, V.¹⁶ Jonker, H.R.A.¹⁷ Kennedy, M.A.¹⁸ Lange, O.F.¹⁹ Liu, G.²⁰ more..

4
- 3543012707
- A. T. Brünger, P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J. S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, G. L. Warren, Acta Crystallogr. D Biol. Crystallogr. 1998, 54, 905-921.
- (1998) Acta Crystallogr. D Biol. Crystallogr. , vol.54 , pp. 905-921
- Brünger, A.T.¹ Adams, P.D.² Clore, G.M.³ Delano, W.L.⁴ Gros, P.⁵ Grosse-Kunstleve, R.W.⁶ Jiang, J.S.⁷ Kuszewski, J.⁸ Nilges, M.⁹ Pannu, N.S.¹⁰ Read, R.J.¹¹ Rice, L.M.¹² Simonson, T.¹³ Warren, G.L.¹⁴

5
- 0027136282
- A. Sali, T. L. Blundell, J. Mol. Biol. 1993, 234, 779.
- (1993) J. Mol. Biol. , vol.234 , pp. 779
- Sali, A.¹ Blundell, T.L.²

6
- 84986512474
- B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, M. Karplus, J. Comp. Chem. 1983, 4, 187.
- (1983) J. Comp. Chem , vol.4 , pp. 187
- Brooks, B.¹ Bruccoleri, R.² Olafson, B.³ States, D.⁴ Swaminathan, S.⁵ Karplus, M.⁶

7
- 46249092554
- B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, J. Chem. Theory Comput. 2008, 4, 435.
- (2008) J. Chem. Theory Comput. , vol.4 , pp. 435
- Hess, B.¹ Kutzner, C.² Van Der Spoel, D.³ Lindahl, E.⁴

8
- 83855162746
- A. -P. E. Kunz, J. R. Allison, D. P. Geerke, B. A. C. Horta, P. H. Hünenberger, S. Riniker, N. Schmid, W. F. van Gunsteren, J. Comput. Chem. 2012, 33, 340.
- (2012) J. Comput. Chem. , vol.33 , pp. 340
- Kunz, A.-P.E.¹ Allison, J.R.² Geerke, D.P.³ Horta, B.A.C.⁴ Hünenberger, P.H.⁵ Riniker, S.⁶ Schmid, N.⁷ Van Gunsteren, W.F.⁸

9
- 23444454552
- D. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J. Comput. Chem. 2005, 26, 1668.
- (2005) J. Comput. Chem. , vol.26 , pp. 1668
- Case, D.A.¹ Cheatham, T.E.² Darden, T.³ Gohlke, H.⁴ Luo, R.⁵ Merz, K.M.⁶ Onufriev, A.⁷ Simmerling, C.⁸ Wang, B.⁹ Woods, R.J.¹⁰

10
- 0013293280
- C. D. Schwieters, J. J. Kuszewski, N. Tjandra, G. M. Clore, J. Magn. Reson. 2003, 160, 65.
- (2003) J. Magn. Reson. , vol.160 , pp. 65
- Schwieters, C.D.¹ Kuszewski, J.J.² Tjandra, N.³ Clore, G.M.⁴

11
- 78650905964
- A. Leaver-Fay, M. Tyka, S. M. Lewis, O. F. Lange, J. Thompson, R. Jacak, K. Kaufman, P. D. Renfrew, C. A. Smith, W. Sheffler, I. W. Davis, S. Cooper, A. Treuille, D. J. Mandell, F. Richter, Y.-E. A. Ban, S. J. Fleishman, J. E. Corn, D. E. Kim, S. Lyskov, M. Berrondo, S. Mentzer, Z. Popovic̈, J. J. Havranek, J. Karanicolas, R. Das, J. Meiler, T. Kortemme, J. J. Gray, B. Kuhlman, D. Baker, P. Bradley, Methods Enzymol. 2011, 487, 545.
- (2011) Methods Enzymol. , vol.487 , pp. 545
- Leaver-Fay, A.¹ Tyka, M.² Lewis, S.M.³ Lange, O.F.⁴ Thompson, J.⁵ Jacak, R.⁶ Kaufman, K.⁷ Renfrew, P.D.⁸ Smith, C.A.⁹ Sheffler, W.¹⁰ Davis, I.W.¹¹ Cooper, S.¹² Treuille, A.¹³ Mandell, D.J.¹⁴ Richter, F.¹⁵ Ban, Y.-E.A.¹⁶ Fleishman, S.J.¹⁷ Corn, J.E.¹⁸ Kim, D.E.¹⁹ Lyskov, S.²⁰ more..

12
- 0025398721
- G. Vriend, J. Mol. Graph. 1990, 8, 52.
- (1990) J. Mol. Graph. , vol.8 , pp. 52
- Vriend, G.¹

13
- 0000243829
- R. A. Laskowski, M. W. MacArthur, D. S. Moss, J. M. Thornton, J. Appl. Crystallogr. 1993, 26, 283.
- (1993) J. Appl. Crystallogr. , vol.26 , pp. 283
- Laskowski, R.A.¹ MacArthur, M.W.² Moss, D.S.³ Thornton, J.M.⁴

14
- 84899435558
- A. Cavalli, X. Salvatella, C. M. Dobson, M. Vendruscolo, Proc. Natl. Acad. Sci. USA 2007, 32, 204.
- (2007) Proc. Natl. Acad. Sci. USA , vol.32 , pp. 204
- Cavalli, A.¹ Salvatella, X.² Dobson, C.M.³ Vendruscolo, M.⁴

15
- 79960909252
- A. Cavalli, R. W. Montalvao, M. Vendruscolo, J. Phys. Chem. B 2011, 115, 9491.
- (2011) J. Phys. Chem. B , vol.115 , pp. 9491
- Cavalli, A.¹ Montalvao, R.W.² Vendruscolo, M.³

16
- 84872620552
- O'Reilly Media Inc., San Francisco, CA
- J. Levine, Flex & Bison; O'Reilly Media Inc., San Francisco, CA, 2009.
- (2009) Flex & Bison
- Levine, J.¹

17
- 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

18
- 0037147531
- R. D. Skeel, J. A. Izaguirre, Mol. Phys. 2002, 100, 3885.
- (2002) Mol. Phys. , vol.100 , pp. 3885
- Skeel, R.D.¹ Izaguirre, J.A.²

19
- 0000040038
- A. Jain, N. Vaidehi, G. Rodriguez, J. Comput. Phys. 1993, 106, 258.
- (1993) J. Comput. Phys. , vol.106 , pp. 258
- Jain, A.¹ Vaidehi, N.² Rodriguez, G.³

20
- 0029633186
- D. Pearlman, D. Case, J. Caldwell, W. Ross, T. Cheatham, S. Debolt, D. Ferguson, G. Seibel, P. Kollman, Comput. Phys. Commun. 1995, 91, 1-41.
- (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
- Pearlman, D.¹ Case, D.² Caldwell, J.³ Ross, W.⁴ Cheatham, T.⁵ Debolt, S.⁶ Ferguson, D.⁷ Seibel, G.⁸ Kollman, P.⁹

21
- 0029912748
- W. Jorgensen, D. Maxwell, J. TiradoRives, J. Am. Chem. Soc. 1996, 118, 11225.
- (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225
- Jorgensen, W.¹ Maxwell, D.² Tiradorives, J.³

22
- 0022596727
- D. Eisenberg, A. D. McLachlan, Nature 1986, 319, 199.
- (1986) Nature , vol.319 , pp. 199
- Eisenberg, D.¹ McLachlan, A.D.²

23
- 0030612335
- N. Tjandra, J. G. Omichinski, A. M. Gronenborn, G. M. Clore, A. Bax, Nat. Struct. Mol. Biol. 1997, 4, 732.
- (1997) Nat. Struct. Mol. Biol. , vol.4 , pp. 732
- Tjandra, N.¹ Omichinski, J.G.² Gronenborn, A.M.³ Clore, G.M.⁴ Bax, A.⁵

24
- 0033135638
- T. Lazaridis, M. Karplus, Proteins 1999, 35, 133.
- (1999) Proteins , vol.35 , pp. 133
- Lazaridis, T.¹ Karplus, M.²

25
- 0033654297
- D. Bashford, D. A. Case, Annu. Rev. Phys. Chem. 2000, 51, 129.
- (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129
- Bashford, D.¹ Case, D.A.²

26
- 70349627256
- K. J. Kohlhoff, P. Robustelli, A. Cavalli, X. Salvatella, M. Vendruscolo, J. Am. Chem. Soc. 2009, 131, 13894.
- (2009) J. Am. Chem. Soc. , vol.131 , pp. 13894
- Kohlhoff, K.J.¹ Robustelli, P.² Cavalli, A.³ Salvatella, X.⁴ Vendruscolo, M.⁵

27
- 80051686715
- A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo, J. Biomol. NMR 2011, 50, 331.
- (2011) J. Biomol. NMR , vol.50 , pp. 331
- Sahakyan, A.B.¹ Vranken, W.F.² Cavalli, A.³ Vendruscolo, M.⁴

28
- 80053507952
- A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo, Angew. Chem. Int. Ed. Engl. 2011, 50, 9620.
- (2011) Angew. Chem. Int. Ed. Engl. , vol.50 , pp. 9620
- Sahakyan, A.B.¹ Vranken, W.F.² Cavalli, A.³ Vendruscolo, M.⁴

29
- 51249118082
- F. Förster, B. Webb, K. A. Krukenberg, H. Tsuruta, D. A. Agard, A. Sali, J. Mol. Biol. 2008, 382, 1089.
- (2008) J. Mol. Biol. , vol.382 , pp. 1089
- Förster, F.¹ Webb, B.² Krukenberg, K.A.³ Tsuruta, H.⁴ Agard, D.A.⁵ Sali, A.⁶

30
- 56749151048
- R. W. Montalvao, A. Cavalli, X. Salvatella, T. L. Blundell, M. Vendruscolo, J. Am. Chem. Soc. 2008, 130, 15990.
- (2008) J. Am. Chem. Soc. , vol.130 , pp. 15990
- Montalvao, R.W.¹ Cavalli, A.² Salvatella, X.³ Blundell, T.L.⁴ Vendruscolo, M.⁵

31
- 0003919736
- Wiley-Interscience
- K. Wüthrich, NMR of Proteins and Nucleic Acids; Wiley-Interscience, 1986.
- (1986) NMR of Proteins and Nucleic Acids
- Wüthrich, K.¹

32
- 58849162221
- P. Güntert, Eur. Biophys. J. 2009, 38, 129.
- (2009) Eur. Biophys. J. , vol.38 , pp. 129
- Güntert, P.¹

33
- 0036308102
- T. Herrmann, P. Güntert, K. Wüthrich, J. Mol. Biol. 2002, 319, 209.
- (2002) J. Mol. Biol. , vol.319 , pp. 209
- Herrmann, T.¹ Güntert, P.² Wüthrich, K.³

34
- 4644340524
- P. Güntert, Methods Mol. Biol. 2004, 278, 353.
- (2004) Methods Mol. Biol. , vol.278 , pp. 353
- Güntert, P.¹

35
- 77955498721
- P. Robustelli, K. Kohlhoff, A. Cavalli, M. Vendruscolo, Structure 2010, 18, 923.
- (2010) Structure , vol.18 , pp. 923
- Robustelli, P.¹ Kohlhoff, K.² Cavalli, A.³ Vendruscolo, M.⁴

36
- 84860013075
- P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundström, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, L. E. Kay, Science 2012, 336, 362.
- (2012) Science , vol.336 , pp. 362
- Neudecker, P.¹ Robustelli, P.² Cavalli, A.³ Walsh, P.⁴ Lundström, P.⁵ Zarrine-Afsar, A.⁶ Sharpe, S.⁷ Vendruscolo, M.⁸ Kay, L.E.⁹

37
- 69349100797
- M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Martinelli, F. Pietrucci, R. A. Broglia, M. Parrinello, Comput. Phys. 2009, 180, 1961.
- (2009) Comput. Phys. , vol.180 , pp. 1961
- Bonomi, M.¹ Branduardi, D.² Bussi, G.³ Camilloni, C.⁴ Provasi, D.⁵ Raiteri, P.⁶ Donadio, D.⁷ Martinelli, F.⁸ Pietrucci, F.⁹ Broglia, R.A.¹⁰ Parrinello, M.¹¹

38
- 84857845204
- C. Camilloni, P. Robustelli, A. De Simone, A. Cavalli, M. Vendruscolo, J. Am. Chem. Soc. 2012, 134, 3968.
- (2012) J. Am. Chem. Soc. , vol.134 , pp. 3968
- Camilloni, C.¹ Robustelli, P.² De Simone, A.³ Cavalli, A.⁴ Vendruscolo, M.⁵

39
- 84873905399
- C. Camilloni, A. Cavalli, M. Vendruscolo, J. Phys. Chem. B 2013, 117, 1838.
- (2013) J. Phys. Chem. B , vol.117 , pp. 1838
- Camilloni, C.¹ Cavalli, A.² Vendruscolo, M.³

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.