-
1
-
-
17844400537
-
How restriction enzymes became the workhorses of molecular biology
-
Roberts, R.J. How restriction enzymes became the workhorses of molecular biology. Proc. Natl. Acad. Sci. USA 102, 5905-5908 (2005).
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5905-5908
-
-
Roberts, R.J.1
-
2
-
-
70349229163
-
On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family
-
Pingoud, V. et al. On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J. Mol. Biol. 393, 140-160 (2009).
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 140-160
-
-
Pingoud, V.1
-
3
-
-
0002598414
-
-
eds. Linn, S.M., Lloyd, R.S. & Roberts, R.J. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
-
Roberts, R.J. & Halford, S.E. in Nucleases (eds. Linn, S.M., Lloyd, R.S. & Roberts, R.J.) 35-88 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1993).
-
(1993)
Nucleases
, pp. 35-88
-
-
Roberts, R.J.1
Halford, S.E.2
-
4
-
-
0020651460
-
Oxygen chiral phosphate esters
-
Gerlt, J.A., Coderre, J.A. & Mehdi, S. Oxygen chiral phosphate esters. Adv. Enzymol. 55, 291-380 (1983).
-
(1983)
Adv. Enzymol.
, vol.55
, pp. 291-380
-
-
Gerlt, J.A.1
Coderre, J.A.2
Mehdi, S.3
-
5
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
Steitz, T.A. & Steitz, J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498-6502 (1993).
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
7
-
-
79951678159
-
Nucleases: Diversity of structure, function and mechanism
-
Yang, W. Nucleases: diversity of structure, function and mechanism. Q. Rev. Biophys. 44, 1-93 (2011).
-
(2011)
Q. Rev. Biophys.
, vol.44
, pp. 1-93
-
-
Yang, W.1
-
8
-
-
77949885922
-
Homing endonucleases: From basics to therapeutic applications
-
Marcaida, M.J., Munoz, I.G., Blanco, F.J., Prieto, J. & Montoya, G. Homing endonucleases: from basics to therapeutic applications. Cell. Mol. Life Sci. 67, 727-748 (2010).
-
(2010)
Cell. Mol. Life Sci.
, vol.67
, pp. 727-748
-
-
Marcaida, M.J.1
Munoz, I.G.2
Blanco, F.J.3
Prieto, J.4
Montoya, G.5
-
9
-
-
33644756595
-
Homing endonuclease structure and function
-
Stoddard, B.L. Homing endonuclease structure and function. Q. Rev. Biophys. 38, 49-95 (2005).
-
(2005)
Q. Rev. Biophys.
, vol.38
, pp. 49-95
-
-
Stoddard, B.L.1
-
10
-
-
28944449341
-
Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets
-
Arnould, S. et al. Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J. Mol. Biol. 355, 443-458 (2006).
-
(2006)
J. Mol. Biol.
, vol.355
, pp. 443-458
-
-
Arnould, S.1
-
11
-
-
33745278855
-
Computational redesign of endonuclease DNA binding and cleavage specificity
-
Ashworth, J. et al. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441, 656-659 (2006).
-
(2006)
Nature
, vol.441
, pp. 656-659
-
-
Ashworth, J.1
-
12
-
-
65349107366
-
Directed evolution of homing endonuclease I-SceI with altered sequence specificity
-
Chen, Z., Wen, F., Sun, N. & Zhao, H. Directed evolution of homing endonuclease I-SceI with altered sequence specificity. Protein Eng. Des. Sel. 22, 249-256 (2009).
-
(2009)
Protein Eng. Des. Sel.
, vol.22
, pp. 249-256
-
-
Chen, Z.1
Wen, F.2
Sun, N.3
Zhao, H.4
-
13
-
-
33750209424
-
Homing endonuclease I-CreI derivatives with novel DNA target specificities
-
Rosen, L.E. et al. Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Res. 34, 4791-4800 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 4791-4800
-
-
Rosen, L.E.1
-
14
-
-
79551491956
-
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
-
Muñoz, I.G. et al. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res. 39, 729-743 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 729-743
-
-
Muñoz, I.G.1
-
15
-
-
55549138062
-
Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases
-
Redondo, P. et al. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature 456, 107-111 (2008).
-
(2008)
Nature
, vol.456
, pp. 107-111
-
-
Redondo, P.1
-
16
-
-
80051964399
-
Tapping natural reservoirs of homing endonucleases for targeted gene modification
-
Takeuchi, R. et al. Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc. Natl. Acad. Sci. USA 108, 13077-13082 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 13077-13082
-
-
Takeuchi, R.1
-
17
-
-
0022407822
-
An intron in the 23S ribosomal gene of the archaebacterium Desulfurococcus mobilis
-
Kjems, J. & Garrett, R.A. An intron in the 23S ribosomal gene of the archaebacterium Desulfurococcus mobilis. Nature 318, 675-677 (1985).
-
(1985)
Nature
, vol.318
, pp. 675-677
-
-
Kjems, J.1
Garrett, R.A.2
-
18
-
-
0027190470
-
A site-specific endonuclease encoded by a typical archaeal intron
-
Dalgaard, J.Z., Garrett, R.A. & Belfort, M. A site-specific endonuclease encoded by a typical archaeal intron. Proc. Natl. Acad. Sci. USA 90, 5414-5417 (1993).
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5414-5417
-
-
Dalgaard, J.Z.1
Garrett, R.A.2
Belfort, M.3
-
19
-
-
0027999532
-
Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron
-
Dalgaard, J.Z., Garrett, R.A. & Belfort, M. Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron. J. Biol. Chem. 269, 28885-28892 (1994).
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 28885-28892
-
-
Dalgaard, J.Z.1
Garrett, R.A.2
Belfort, M.3
-
20
-
-
0035883706
-
Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility
-
Chevalier, B.S. & Stoddard, B.L. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res. 29, 3757-3774 (2001).
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3757-3774
-
-
Chevalier, B.S.1
Stoddard, B.L.2
-
21
-
-
55949101131
-
Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering
-
Marcaida, M.J. et al. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc. Natl. Acad. Sci. USA 105, 16888-16893 (2008).
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 16888-16893
-
-
Marcaida, M.J.1
-
22
-
-
0346030573
-
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor
-
Bolduc, J.M. et al. Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev. 17, 2875-2888 (2003).
-
(2003)
Genes Dev.
, vol.17
, pp. 2875-2888
-
-
Bolduc, J.M.1
-
23
-
-
8344256614
-
Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease
-
Chevalier, B. et al. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 43, 14015-14026 (2004).
-
(2004)
Biochemistry
, vol.43
, pp. 14015-14026
-
-
Chevalier, B.1
-
24
-
-
0242636378
-
The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity
-
Moure, C.M., Gimble, F.S. & Quiocho, F.A. The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J. Mol. Biol. 334, 685-695 (2003).
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 685-695
-
-
Moure, C.M.1
Gimble, F.S.2
Quiocho, F.A.3
-
25
-
-
84879897415
-
Observing a DNA polymerase choose right from wrong
-
Freudenthal, B.D., Beard, W.A., Shock, D.D. & Wilson, S.H. Observing a DNA polymerase choose right from wrong. Cell 154, 157-168 (2013).
-
(2013)
Cell
, vol.154
, pp. 157-168
-
-
Freudenthal, B.D.1
Beard, W.A.2
Shock, D.D.3
Wilson, S.H.4
-
26
-
-
84863676249
-
Watching DNA polymerase • make a phosphodiester bond
-
Nakamura, T., Zhao, Y., Yamagata, Y., Hua, Y.J. & Yang, W. Watching DNA polymerase • make a phosphodiester bond. Nature 487, 196-201 (2012).
-
(2012)
Nature
, vol.487
, pp. 196-201
-
-
Nakamura, T.1
Zhao, Y.2
Yamagata, Y.3
Hua, Y.J.4
Yang, W.5
-
27
-
-
42949157474
-
Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease
-
Prieto, J. et al. Generation and analysis of mesophilic variants of the thermostable archaeal I-DmoI homing endonuclease. J. Biol. Chem. 283, 4364-4374 (2008).
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 4364-4374
-
-
Prieto, J.1
-
28
-
-
0031004765
-
Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism
-
Pontius, B.W., Lott, W.B. & von Hippel, P.H. Observations on catalysis by hammerhead ribozymes are consistent with a two-divalent-metal-ion mechanism. Proc. Natl. Acad. Sci. USA 94, 2290-2294 (1997).
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 2290-2294
-
-
Pontius, B.W.1
Lott, W.B.2
Von Hippel, P.H.3
-
29
-
-
77955011838
-
Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1: Insights from quantum chemical calculations
-
Liao, R.-Z., Yu, J.-G. & Himo, F. Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1: insights from quantum chemical calculations. Inorg. Chem. 49, 6883-6888 (2010).
-
(2010)
Inorg. Chem.
, vol.49
, pp. 6883-6888
-
-
Liao, R.-Z.1
Yu, J.-G.2
Himo, F.3
-
30
-
-
33846799362
-
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV
-
Ivanov, I., Tainer, J. & McCammon, J. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc. Natl. Acad. Sci. USA 104, 1465-1470 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 1465-1470
-
-
Ivanov, I.1
Tainer, J.2
McCammon, J.3
-
31
-
-
0036810246
-
Design, activity, and structure of a highly specific artificial endonuclease
-
Chevalier, B.S. et al. Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell 10, 895-905 (2002).
-
(2002)
Mol. Cell
, vol.10
, pp. 895-905
-
-
Chevalier, B.S.1
-
32
-
-
0035576327
-
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
-
Gelpí, J.L. et al. Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins. Proteins 45, 428-437 (2001).
-
(2001)
Proteins
, vol.45
, pp. 428-437
-
-
Gelpí, J.L.1
-
33
-
-
34147107263
-
PELE: Protein energy landscape exploration: A novel Monte Carlo based technique
-
Borrelli, W.K., Vitalis, A., Alcantara, R. & Guallar, V. PELE: protein energy landscape exploration: a novel Monte Carlo based technique. J. Chem. Theory Comput. 1, 1304-1311 (2005).
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 1304-1311
-
-
Borrelli, W.K.1
Vitalis, A.2
Alcantara, R.3
Guallar, V.4
-
34
-
-
45549091435
-
Crystal structures of I-SceI complexed to nicked DNA substrates: Snapshots of intermediates along the DNA cleavage reaction pathway
-
Moure, C.M., Gimble, F.S. & Quiocho, F.A. Crystal structures of I-SceI complexed to nicked DNA substrates: snapshots of intermediates along the DNA cleavage reaction pathway. Nucleic Acids Res. 36, 3287-3296 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 3287-3296
-
-
Moure, C.M.1
Gimble, F.S.2
Quiocho, F.A.3
-
35
-
-
84858218497
-
Retaining glycosyltransferase mechanism studied by QM/MM methods: Lipopolysaccharyl-±-1,4-galactosyltransferase C transfers ±-galactose via an oxocarbenium ion-like transition state
-
Gómez, H., Polyak, I., Thiel, W., Lluch, J.M. & Masgrau, L. Retaining glycosyltransferase mechanism studied by QM/MM methods: lipopolysaccharyl-±-1,4-galactosyltransferase C transfers ±-galactose via an oxocarbenium ion-like transition state. J. Am. Chem. Soc. 134, 4743-4752 (2012).
-
(2012)
J. Am. Chem. Soc.
, vol.134
, pp. 4743-4752
-
-
Gómez, H.1
Polyak, I.2
Thiel, W.3
Lluch, J.M.4
Masgrau, L.5
-
36
-
-
84877299428
-
Substrate-assisted and nucleophilically assisted catalysis in bovine α-1,3-galactosyltransferase: Mechanistic implications for retaining glycosyltransferases
-
Gómez, H., Lluch, J.M. & Masgrau, L. Substrate-assisted and nucleophilically assisted catalysis in bovine α-1,3-galactosyltransferase: mechanistic implications for retaining glycosyltransferases. J. Am. Chem. Soc. 135, 7053-7063 (2013).
-
(2013)
J. Am. Chem. Soc.
, vol.135
, pp. 7053-7063
-
-
Gómez, H.1
Lluch, J.M.2
Masgrau, L.3
-
37
-
-
84898075763
-
Computational and experimental study of O-glycosylation: Catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2
-
Gómez, H. et al. Computational and experimental study of O-glycosylation: catalysis by human UDP-GalNAc polypeptide:GalNAc transferase-T2. Org. Biomol. Chem. 12, 2645-2655 (2014).
-
(2014)
Org. Biomol. Chem.
, vol.12
, pp. 2645-2655
-
-
Gómez, H.1
-
38
-
-
79958776843
-
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations
-
Rosta, E., Nowotny, M., Yang, W. & Hummer, G. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J. Am. Chem. Soc. 133, 8934-8941 (2011).
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 8934-8941
-
-
Rosta, E.1
Nowotny, M.2
Yang, W.3
Hummer, G.4
-
39
-
-
84962428752
-
Density functional study of the phosphate diester hydrolysis of RNA in RNA/DNA hybrid by RNase HI
-
Makoto, K., Haruki, N. & Yu, T. Density functional study of the phosphate diester hydrolysis of RNA in RNA/DNA hybrid by RNase HI. Mol. Phys. 112, 355-364 (2014).
-
(2014)
Mol. Phys.
, vol.112
, pp. 355-364
-
-
Makoto, K.1
Haruki, N.2
Yu, T.3
-
40
-
-
50249094329
-
Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism
-
De Vivo, M., Dal Peraro, M. & Klein, M. Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism. J. Am. Chem. Soc. 130, 10955-10962 (2008).
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 10955-10962
-
-
De Vivo, M.1
Dal Peraro, M.2
Klein, M.3
-
41
-
-
77956306804
-
Atomistic details of the associative phosphodiester cleavage in human ribonuclease H
-
Elsässer, B. & Fels, G. Atomistic details of the associative phosphodiester cleavage in human ribonuclease H. Phys. Chem. Chem. Phys. 12, 11081-11088 (2010).
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 11081-11088
-
-
Elsässer, B.1
Fels, G.2
-
42
-
-
0027963590
-
Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase
-
Ding, X., Rasmussen, B.F., Petsko, G.A. & Ringe, D. Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Biochemistry 33, 9285-9293 (1994).
-
(1994)
Biochemistry
, vol.33
, pp. 9285-9293
-
-
Ding, X.1
Rasmussen, B.F.2
Petsko, G.A.3
Ringe, D.4
-
43
-
-
33750725424
-
Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: Exploiting the "glass transition" in protein dynamics
-
Ding, X., Rasmussen, B.F., Petsko, G.A. & Ringe, D. Direct crystallographic observation of an acyl-enzyme intermediate in the elastase-catalyzed hydrolysis of a peptidyl ester substrate: exploiting the "glass transition" in protein dynamics. Bioorg. Chem. 34, 410-423 (2006).
-
(2006)
Bioorg. Chem.
, vol.34
, pp. 410-423
-
-
Ding, X.1
Rasmussen, B.F.2
Petsko, G.A.3
Ringe, D.4
-
44
-
-
0033860560
-
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction
-
Murray, J.B., Szoke, H., Szoke, A. & Scott, W.G. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol. Cell 5, 279-287 (2000).
-
(2000)
Mol. Cell
, vol.5
, pp. 279-287
-
-
Murray, J.B.1
Szoke, H.2
Szoke, A.3
Scott, W.G.4
-
45
-
-
0030476765
-
Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
-
Scott, W.G., Murray, J.B., Arnold, J.R., Stoddard, B.L. & Klug, A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274, 2065-2069 (1996).
-
(1996)
Science
, vol.274
, pp. 2065-2069
-
-
Scott, W.G.1
Murray, J.B.2
Arnold, J.R.3
Stoddard, B.L.4
Klug, A.5
-
46
-
-
36849088130
-
Crystallization and preliminary X-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA
-
Redondo, P., Prieto, J., Ramos, E., Blanco, F.J. & Montoya, G. Crystallization and preliminary X-ray diffraction analysis on the homing endonuclease I-Dmo-I in complex with its target DNA. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63, 1017-1020 (2007).
-
(2007)
Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
, vol.63
, pp. 1017-1020
-
-
Redondo, P.1
Prieto, J.2
Ramos, E.3
Blanco, F.J.4
Montoya, G.5
-
49
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.J.1
-
51
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
-
(2010)
Acta Crystallogr. D Biol. Crystallogr.
, vol.66
, pp. 213-221
-
-
Adams, P.D.1
-
52
-
-
0019182556
-
The EcoRI restriction endonuclease with bacteriophage λ DNA: Kinetic studies
-
Halford, S.E., Johnson, N.P. & Grinsted, J. The EcoRI restriction endonuclease with bacteriophage λ DNA: kinetic studies. Biochem. J. 191, 581-592 (1980).
-
(1980)
Biochem. J.
, vol.191
, pp. 581-592
-
-
Halford, S.E.1
Johnson, N.P.2
Grinsted, J.3
-
53
-
-
23144457576
-
as and adding missing hydrogens to macromolecules
-
as and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33, W368-W371 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. W368-W371
-
-
Gordon, J.C.1
-
54
-
-
33646794930
-
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
-
Myers, J., Grothaus, G., Narayanan, S. & Onufriev, A. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins 63, 928-938 (2006).
-
(2006)
Proteins
, vol.63
, pp. 928-938
-
-
Myers, J.1
Grothaus, G.2
Narayanan, S.3
Onufriev, A.4
-
55
-
-
84864473993
-
3.0: Automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
-
Anandakrishnan, R., Aguilar, B. & Onufriev, A. H. 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40, W537-W541 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W537-W541
-
-
Anandakrishnan, R.1
Aguilar, B.2
Onufriev, A.H.3
-
56
-
-
0242391123
-
QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis
-
Sherwood, P. et al. QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis. J. Mol. Struct. Theochem. 632, 1-28 (2003).
-
(2003)
J. Mol. Struct. Theochem.
, vol.632
, pp. 1-28
-
-
Sherwood, P.1
-
57
-
-
4243539377
-
Electronic structure calculations on workstation computers: The program system turbomole
-
Ahlrichs, R., Bär, M., Häser, M., Horn, H. & Kölmel, C. Electronic structure calculations on workstation computers: the program system turbomole. Chem. Phys. Lett. 162, 165-169 (1989).
-
(1989)
Chem. Phys. Lett.
, vol.162
, pp. 165-169
-
-
Ahlrichs, R.1
Bär, M.2
Häser, M.3
Horn, H.4
Kölmel, C.5
-
58
-
-
33846410438
-
A simplification of the Hartree-Fock method
-
Slater, J.C. A simplification of the Hartree-Fock method. Phys. Rev. 81, 385-390 (1951).
-
(1951)
Phys. Rev.
, vol.81
, pp. 385-390
-
-
Slater, J.C.1
-
59
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behavior
-
Becke, A.D. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 38, 3098-3100 (1988).
-
(1988)
Phys. Rev. A
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
60
-
-
34250817103
-
A new mixing of Hartree-Fock and local density-functional theories
-
Becke, A.D. A new mixing of Hartree-Fock and local density-functional theories. J. Chem. Phys. 98, 1372-1377 (1993).
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 1372-1377
-
-
Becke, A.D.1
-
61
-
-
33751157732
-
Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields
-
Stephens, P.J., Devlin, F.J., Chabalowski, C.F. & Frisch, M.J. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98, 11623-11627 (1994).
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 11623-11627
-
-
Stephens, P.J.1
Devlin, F.J.2
Chabalowski, C.F.3
Frisch, M.J.4
-
62
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
-
Lee, C., Yang, W. & Parr, R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B Condens. Matter 37, 785-789 (1988).
-
(1988)
Phys. Rev. B Condens. Matter
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
63
-
-
26344435738
-
Fully optimized contracted Gaussian basis sets for atoms Li to Kr
-
Schäfer, A., Horn, H. & Ahlrichs, R. Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys. 97, 2571-2577 (1992).
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 2571-2577
-
-
Schäfer, A.1
Horn, H.2
Ahlrichs, R.3
-
64
-
-
84986468715
-
Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F
-
Clark, T., Chandrasekhar, J., Spitznagel, G.W. & Schleyer, P.V.R. Efficient diffuse function-augmented basis sets for anion calculations. III. The 3-21+G basis set for first-row elements, Li-F. J. Comput. Chem. 4, 294-301 (1983).
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 294-301
-
-
Clark, T.1
Chandrasekhar, J.2
Spitznagel, G.W.3
Schleyer, P.V.R.4
-
65
-
-
0030175155
-
DL-POLY-2.0: A general-purpose parallel molecular dynamics simulation package
-
Smith, W. & Forester, T. DL-POLY-2.0: a general-purpose parallel molecular dynamics simulation package. J. Mol. Graph. 14, 136-141 (1996).
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 136-141
-
-
Smith, W.1
Forester, T.2
-
66
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Scott, J.W. et al. A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784 (1984).
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Scott, J.W.1
-
67
-
-
0345713551
-
Hybrid models for combined quantum mechanical and molecular mechanical approaches
-
Dirk, B. & Walter, T. Hybrid models for combined quantum mechanical and molecular mechanical approaches. J. Phys. Chem. 100, 10580-10594 (1996).
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 10580-10594
-
-
Dirk, B.1
Walter, T.2
-
68
-
-
2742608402
-
Computer simulation of zeolite structure and reactivity using embedded cluster methods
-
Sherwood, P. et al. Computer simulation of zeolite structure and reactivity using embedded cluster methods. Faraday Discuss. 106, 79-92 (1997).
-
(1997)
Faraday Discuss.
, vol.106
, pp. 79-92
-
-
Sherwood, P.1
-
69
-
-
84966262179
-
Updating quasi-Newton matrices with limited storage
-
Nocedal, J. Updating quasi-Newton matrices with limited storage. Math. Comput. 35, 773-782 (1980).
-
(1980)
Math. Comput.
, vol.35
, pp. 773-782
-
-
Nocedal, J.1
-
70
-
-
0039047376
-
Search for stationary points on surfaces
-
Banerjee, A., Adams, N., Simons, J. & Shepard, R. Search for stationary points on surfaces. J. Phys. Chem. 89, 52-57 (1985).
-
(1985)
J. Phys. Chem.
, vol.89
, pp. 52-57
-
-
Banerjee, A.1
Adams, N.2
Simons, J.3
Shepard, R.4
-
71
-
-
84988122931
-
An algorithm for the location of transition states
-
Baker, J. An algorithm for the location of transition states. J. Comput. Chem. 7, 385-395 (1986).
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 385-395
-
-
Baker, J.1
-
72
-
-
0034658025
-
Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates
-
Billeter, S.R., Turner, A.J. & Thiel, W. Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates. Phys. Chem. Chem. Phys. 2, 2177-2186 (2000).
-
(2000)
Phys. Chem. Chem. Phys.
, vol.2
, pp. 2177-2186
-
-
Billeter, S.R.1
Turner, A.J.2
Thiel, W.3
-
73
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N.A., Sept, D., Joseph, S., Holst, M.J. & McCammon, J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 (2001).
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
74
-
-
79956001462
-
Substrate diffusion and oxidation in GMC oxidoreductases: An experimental and computational study on fungal aryl-alcohol oxidase
-
Hernández-Ortega, A. et al. Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase. Biochem. J. 436, 341-350 (2011).
-
(2011)
Biochem. J.
, vol.436
, pp. 341-350
-
-
Hernández-Ortega, A.1
-
75
-
-
84921450377
-
Atomic picture of ligand migration in toluene 4-monooxygenase
-
13 May
-
Hosseini, A. et al. Atomic picture of ligand migration in toluene 4-monooxygenase. J. Phys. Chem. B (doi:10.1021/jp502509a) (13 May 2014).
-
(2014)
J. Phys. Chem. B
-
-
Hosseini, A.1
-
76
-
-
84857324414
-
An atomistic view on human hemoglobin carbon monoxide migration processes
-
Lucas, M.F. & Guallar, V. An atomistic view on human hemoglobin carbon monoxide migration processes. Biophys. J. 102, 887-896 (2012).
-
(2012)
Biophys. J.
, vol.102
, pp. 887-896
-
-
Lucas, M.F.1
Guallar, V.2
-
77
-
-
84884666993
-
Single vs. multiple ligand pathways in globins: A computational view
-
Lucas, M.F. & Guallar, V. Single vs. multiple ligand pathways in globins: a computational view. Biochim. Biophys. Acta 1834, 1739-1743 (2013).
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 1739-1743
-
-
Lucas, M.F.1
Guallar, V.2
-
78
-
-
84884666066
-
Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2
-
Spyrakis, F. et al. Comparative analysis of inner cavities and ligand migration in non-symbiotic AHb1 and AHb2. Biochim. Biophys. Acta 1834, 1957-1967 (2013).
-
(2013)
Biochim. Biophys. Acta
, vol.1834
, pp. 1957-1967
-
-
Spyrakis, F.1
-
79
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak, V. et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725 (2006).
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
-
80
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Pérez, A. et al. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J. 92, 3817-3829 (2007).
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Pérez, A.1
-
81
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified generalized born model
-
Onufriev, A., Bashford, D. & Case, D.A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55, 383-394 (2004).
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
82
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996).
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
|