-
1
-
-
84655171824
-
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
-
Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV, (2012) Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 112: 632-672.
-
(2012)
Chem Rev
, vol.112
, pp. 632-672
-
-
Gordon, M.S.1
Fedorov, D.G.2
Pruitt, S.R.3
Slipchenko, L.V.4
-
2
-
-
5244276541
-
Energy components of aqueous solution: insight from hybrid qm/mm simulations using a polarizable solvent model
-
Gao J, (1997) Energy components of aqueous solution: insight from hybrid qm/mm simulations using a polarizable solvent model. J Comput Chem 18: 1061-1071.
-
(1997)
J Comput Chem
, vol.18
, pp. 1061-1071
-
-
Gao, J.1
-
3
-
-
36649021120
-
The design of a next generation force field: the x-pol potential
-
Xie W, Gao J, (2007) The design of a next generation force field: the x-pol potential. J Chem Theory Comput 3: 1890-1900.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 1890-1900
-
-
Xie, W.1
Gao, J.2
-
4
-
-
67650076137
-
Thermochemical fragment energy method for biomolecules: Application to a collagen model peptide
-
Suáez E, Díaz N, Suárez D, (2009) Thermochemical fragment energy method for biomolecules: Application to a collagen model peptide. J Chem Theory Comput 5: 1667-1679.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 1667-1679
-
-
Suáez, E.1
Díaz, N.2
Suárez, D.3
-
5
-
-
34548243709
-
Extending the power of quantum chemistry to large systems with the fragment molecular orbital method
-
Fedorov D, Kitaura K, (2007) Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. J Phys Chem A 111: 6904-6914.
-
(2007)
J Phys Chem A
, vol.111
, pp. 6904-6914
-
-
Fedorov, D.1
Kitaura, K.2
-
7
-
-
79955926989
-
Molecules-in-molecules: An extrapolated fragment-based approach for accurate calculations on large molecules and materials
-
10.1021/ct200033b
-
Mayhall NJ, Raghavachari K, (2011) Molecules-in-molecules: An extrapolated fragment-based approach for accurate calculations on large molecules and materials. J Chem Theory Comput 7: 1336-1343 doi:10.1021/ct200033b.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 1336-1343
-
-
Mayhall, N.J.1
Raghavachari, K.2
-
8
-
-
77955916844
-
Effective fragment molecular orbital method: A merger of the effective fragment potential and fragment molecular orbital methods
-
Steinmann C, Fedorov DG, Jensen JH, (2010) Effective fragment molecular orbital method: A merger of the effective fragment potential and fragment molecular orbital methods. J Phys Chem A 114: 8705-8712.
-
(2010)
J Phys Chem A
, vol.114
, pp. 8705-8712
-
-
Steinmann, C.1
Fedorov, D.G.2
Jensen, J.H.3
-
9
-
-
84864204969
-
The effective fragment molecular orbital method for fragments connected by covalent bonds
-
10.1371/journal.pone.0041117
-
Steinmann C, Fedorov DG, Jensen JH, (2012) The effective fragment molecular orbital method for fragments connected by covalent bonds. PLoS ONE 7: e41117 doi:10.1371/journal.pone.0041117.
-
(2012)
PLoS ONE
, vol.7
-
-
Steinmann, C.1
Fedorov, D.G.2
Jensen, J.H.3
-
10
-
-
33845302986
-
The three-body fragment molecular orbital method for accurate calculations of large systems
-
Fedorov D, Kitaura K, (2006) The three-body fragment molecular orbital method for accurate calculations of large systems. Chem Phys Lett 433: 182-187.
-
(2006)
Chem Phys Lett
, vol.433
, pp. 182-187
-
-
Fedorov, D.1
Kitaura, K.2
-
11
-
-
4344708244
-
Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method
-
Fedorov D, Kitaura K, (2004) Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method. J Chem Phys 121: 2483.
-
(2004)
J Chem Phys
, vol.121
, pp. 2483
-
-
Fedorov, D.1
Kitaura, K.2
-
12
-
-
26444532309
-
Coupled-cluster theory based upon the fragment molecular-orbital method
-
Fedorov D, Kitaura K, (2005) Coupled-cluster theory based upon the fragment molecular-orbital method. J Chem Phys 123: 134103.
-
(2005)
J Chem Phys
, vol.123
, pp. 134103
-
-
Fedorov, D.1
Kitaura, K.2
-
13
-
-
34249808523
-
Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory
-
Fedorov D, Ishimura K, Ishida T, Kitaura K, Pulay P, et al. (2007) Accuracy of the three-body fragment molecular orbital method applied to Møller-Plesset perturbation theory. J Comput Chem 28: 1476-1484.
-
(2007)
J Comput Chem
, vol.28
, pp. 1476-1484
-
-
Fedorov, D.1
Ishimura, K.2
Ishida, T.3
Kitaura, K.4
Pulay, P.5
-
14
-
-
34548683709
-
Time-dependent density functional theory based upon the fragment molecular orbital method
-
Chiba M, Fedorov D, Kitaura K, (2007) Time-dependent density functional theory based upon the fragment molecular orbital method. J Chem Phys 127: 104-108.
-
(2007)
J Chem Phys
, vol.127
, pp. 104-108
-
-
Chiba, M.1
Fedorov, D.2
Kitaura, K.3
-
15
-
-
84893169025
-
General atomic and molecular electronic structure system
-
Schmidt M, Baldridge K, Boatz J, Elbert S, Gordon M, et al. (1993) General atomic and molecular electronic structure system. J Comput Chem 14: 1347-1363.
-
(1993)
J Comput Chem
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.1
Baldridge, K.2
Boatz, J.3
Elbert, S.4
Gordon, M.5
-
16
-
-
1942423116
-
A new hierarchical parallelization scheme: Generalized distributed data interface (gddi), and an application to the fragment molecular orbital method (fmo)
-
Fedorov D, Olson R, Kitaura K, Gordon M, Koseki S, (2004) A new hierarchical parallelization scheme: Generalized distributed data interface (gddi), and an application to the fragment molecular orbital method (fmo). J Comput Chem 25: 872-880.
-
(2004)
J Comput Chem
, vol.25
, pp. 872-880
-
-
Fedorov, D.1
Olson, R.2
Kitaura, K.3
Gordon, M.4
Koseki, S.5
-
17
-
-
84855715655
-
Large-scale mp2 calculations on the blue gene architecture using the fragment molecular orbital method
-
Fletcher G, Fedorov D, Pruitt S, Windus T, Gordon M, (2012) Large-scale mp2 calculations on the blue gene architecture using the fragment molecular orbital method. J Chem Theory Comput.
-
(2012)
J Chem Theory Comput
-
-
Fletcher, G.1
Fedorov, D.2
Pruitt, S.3
Windus, T.4
Gordon, M.5
-
18
-
-
0001046021
-
Fragment molecular orbital method: application to polypeptides
-
Nakano T, Kaminuma T, Sato T, Akiyama Y, Uebayasi M, et al. (2000) Fragment molecular orbital method: application to polypeptides. Chem Phys Lett 318: 614-618.
-
(2000)
Chem Phys Lett
, vol.318
, pp. 614-618
-
-
Nakano, T.1
Kaminuma, T.2
Sato, T.3
Akiyama, Y.4
Uebayasi, M.5
-
19
-
-
57149138044
-
Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method
-
Fedorov D, Jensen J, Deka R, Kitaura K, (2008) Covalent bond fragmentation suitable to describe solids in the fragment molecular orbital method. J Phys Chem A 112: 11808-11816.
-
(2008)
J Phys Chem A
, vol.112
, pp. 11808-11816
-
-
Fedorov, D.1
Jensen, J.2
Deka, R.3
Kitaura, K.4
-
20
-
-
67650763997
-
Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method
-
Fedorov D, Avramov P, Jensen J, Kitaura K, (2009) Analytic gradient for the adaptive frozen orbital bond detachment in the fragment molecular orbital method. Chem Phys Lett 477: 169-175.
-
(2009)
Chem Phys Lett
, vol.477
, pp. 169-175
-
-
Fedorov, D.1
Avramov, P.2
Jensen, J.3
Kitaura, K.4
-
21
-
-
15744373592
-
Multilayer formulation of the fragment molecular orbital method (fmo)
-
Fedorov D, Ishida T, Kitaura K, (2005) Multilayer formulation of the fragment molecular orbital method (fmo). J Phys Chem A 109: 2638-2646.
-
(2005)
J Phys Chem A
, vol.109
, pp. 2638-2646
-
-
Fedorov, D.1
Ishida, T.2
Kitaura, K.3
-
22
-
-
31144441067
-
Oniom: A multilayered integrated mo+ mm method for geometry optimizations and single point energy predictions. a test for diels-alder reactions and pt (p (t-bu) 3) 2+ h2 oxidative addition
-
Svensson M, Humbel S, Froese R, Matsubara T, Sieber S, et al. (1996) Oniom: A multilayered integrated mo+ mm method for geometry optimizations and single point energy predictions. a test for diels-alder reactions and pt (p (t-bu) 3) 2+ h2 oxidative addition. J Phys Chem 100: 19357-19363.
-
(1996)
J Phys Chem
, vol.100
, pp. 19357-19363
-
-
Svensson, M.1
Humbel, S.2
Froese, R.3
Matsubara, T.4
Sieber, S.5
-
23
-
-
0033515394
-
A new oniom implementation in gaussian98. part i. the calculation of energies, gradients, vibrational frequencies and electric field derivatives
-
Dapprich S, Komáromi I, Byun K, Morokuma K, Frisch M, (1999) A new oniom implementation in gaussian98. part i. the calculation of energies, gradients, vibrational frequencies and electric field derivatives. J Mol Struc-Theochem 461: 1-21.
-
(1999)
J Mol Struc-Theochem
, vol.461
, pp. 1-21
-
-
Dapprich, S.1
Komáromi, I.2
Byun, K.3
Morokuma, K.4
Frisch, M.5
-
24
-
-
84875117743
-
-
Fmoutil v. 2.1. URL http://staff.aist.go.jp/d.g.fedorov/fmo/fmoutil.html. Accessed 2012 August 1.
-
-
-
-
25
-
-
33748790698
-
Facio: new computational chemistry environment for pc gamess
-
Suenaga M, (2005) Facio: new computational chemistry environment for pc gamess. J Comput Chem Jpn 4: 25-32.
-
(2005)
J Comput Chem Jpn
, vol.4
, pp. 25-32
-
-
Suenaga, M.1
-
26
-
-
67650754298
-
Development of gui for gamess/fmo calculation
-
Suenaga M, (2008) Development of gui for gamess/fmo calculation. J Comput Chem Jpn 7: 33-53.
-
(2008)
J Comput Chem Jpn
, vol.7
, pp. 33-53
-
-
Suenaga, M.1
-
27
-
-
3242886771
-
Pdb2pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations
-
Dolinsky T, Nielsen J, McCammon J, Baker N, (2004) Pdb2pqr: an automated pipeline for the setup of poisson-boltzmann electrostatics calculations. Nucleic Acids Res 32: W665.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Dolinsky, T.1
Nielsen, J.2
McCammon, J.3
Baker, N.4
-
28
-
-
34547559704
-
Pdb2pqr: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky T, Czodrowski P, Li H, Nielsen J, Jensen J, et al. (2007) Pdb2pqr: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35: W522.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Dolinsky, T.1
Czodrowski, P.2
Li, H.3
Nielsen, J.4
Jensen, J.5
-
29
-
-
0032058905
-
Recap retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry
-
Lewell X, Judd D, Watson S, Hann M, (1998) Recap retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J Chem Inf Comp Sci 38: 511-522.
-
(1998)
J Chem Inf Comp Sci
, vol.38
, pp. 511-522
-
-
Lewell, X.1
Judd, D.2
Watson, S.3
Hann, M.4
-
30
-
-
80053512597
-
Open babel: An open chemical toolbox
-
O'Boyle N, Banck M, James C, Morley C, Vandermeersch T, et al. (2011) Open babel: An open chemical toolbox. J Cheminf 3: 33.
-
(2011)
J Cheminf
, vol.3
, pp. 33
-
-
O'Boyle, N.1
Banck, M.2
James, C.3
Morley, C.4
Vandermeersch, T.5
-
31
-
-
84875093496
-
-
Openbabel
-
Openbabel v.2.3.0. URL http://openbabel.sourceforge.net. Accessed 2012 August 2.
-
Openbabel
-
-
-
32
-
-
0004117251
-
-
version 4.9. Aliso Viejo, CA, Daylight Chemical Information Systems Inc [Online] Available
-
James C, Weininger D (2006) Daylight theory manual, version 4.9. Aliso Viejo, CA, Daylight Chemical Information Systems Inc [Online] Available: http://www.daylight.com/dayhtml/doc/theory Accessed 2012 August 2.
-
(2006)
Daylight theory manual
-
-
James, C.1
Weininger, D.2
-
33
-
-
84875090175
-
-
Accessed 2012 May 18
-
Python. URL http://www.python.org. Accessed 2012 May 18.
-
Python
-
-
-
34
-
-
84875092441
-
-
Swig. URL http://www.swig.org. Accessed 2012 July 6.
-
Swig
-
-
-
35
-
-
41249098782
-
-
Openbabel python. URL http://openbabel.sourceforge.net/wiki/Python. Accessed 2012 August 2.
-
Openbabel python
-
-
-
36
-
-
79951909482
-
Geometry optimization of the active site of a large system with the fragment molecular orbital method
-
Fedorov D, Alexeev Y, Kitaura K, (2011) Geometry optimization of the active site of a large system with the fragment molecular orbital method. J Phys Chem Lett 2: 282-288.
-
(2011)
J Phys Chem Lett
, vol.2
, pp. 282-288
-
-
Fedorov, D.1
Alexeev, Y.2
Kitaura, K.3
-
39
-
-
84875110646
-
-
georgia state university
-
Glactone, georgia state university. URL http://chemistry.gsu.edu/Glactone/PDB/pdb.html. Accessed 2012 August 2.
-
Glactone
-
-
-
40
-
-
84875084283
-
-
v.1.0.3, Accessed 2012 August 2
-
Avogadro v.1.0.3. URL http://avogadro.openmolecules.net. Accessed 2012 August 2.
-
Avogadro
-
-
-
41
-
-
0037122848
-
Fragment molecular orbital method: use of approximate electrostatic potential
-
Nakano T, Kaminuma T, Sato T, Fukuzawa K, Akiyama Y, et al. (2002) Fragment molecular orbital method: use of approximate electrostatic potential. Chem Phys Lett 351: 475-480.
-
(2002)
Chem Phys Lett
, vol.351
, pp. 475-480
-
-
Nakano, T.1
Kaminuma, T.2
Sato, T.3
Fukuzawa, K.4
Akiyama, Y.5
-
42
-
-
2342622178
-
The importance of three-body terms in the fragment molecular orbital method
-
Fedorov D, Kitaura K, (2004) The importance of three-body terms in the fragment molecular orbital method. J Chem Phys 120: 6832.
-
(2004)
J Chem Phys
, vol.120
, pp. 6832
-
-
Fedorov, D.1
Kitaura, K.2
-
43
-
-
84875090817
-
-
Numpy. URL http://numpy.scipy.org. Accessed 2012 May 18.
-
Numpy
-
-
-
44
-
-
84875120793
-
-
Fragit web service
-
Fragit web service. URL http://www.fragit.org. Accessed 2012 August 7.
-
-
-
|