-
1
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon J (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9:646-652
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.2
-
2
-
-
33746271105
-
Biomolecular modeling: Goals, problems, perspectives
-
van Gunsteren WF et al. (2006) Biomolecular modeling: goals, problems, perspectives. Angew Chemie Int Ed 45:4064-4092
-
(2006)
Angew Chemie Int Ed
, vol.45
, pp. 4064-4092
-
-
Van Gunsteren, W.F.1
-
3
-
-
0041784950
-
All-Atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A et al. (1998) All-Atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.1
-
4
-
-
0003544049
-
-
vdf Hochschulverlag, ETH Zurich
-
van Gunsteren WF, Billeter SR, Eising AA, Hunenberger PH, Kruger P, Mark AE, Scott WRP, Tironi IG (1996) Biomolecular simulation: the GROMOS manual and user guide. vdf Hochschulverlag, ETH Zurich
-
(1996)
Biomolecular Simulation: The GROMOS manual and user guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hunenberger, P.H.4
Kruger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
5
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, Wriggers W (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
Eastwood, M.P.6
Bank, J.A.7
Jumper, J.M.8
Salmon, J.K.9
Shan, Y.10
Wriggers, W.11
-
6
-
-
0001257583
-
Construction of tightbinding-like potentials on the basis of densityfunctional theory -Application to carbon
-
Porezag D, Frauenheim T, Kohler T, Seifert G, Kaschner R (1995) Construction of tightbinding-like potentials on the basis of densityfunctional theory -Application to carbon. Phys Rev B 51:12947-12957
-
(1995)
Phys Rev B
, vol.51
, pp. 12947-12957
-
-
Porezag, D.1
Frauenheim, T.2
Kohler, T.3
Seifert, G.4
Kaschner, R.5
-
7
-
-
1542779956
-
Self-consistent-charge densityfunctional tight-binding method for simulations of complex materials properties
-
Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Self-consistent-charge densityfunctional tight-binding method for simulations of complex materials properties. Phys Rev B 58:7260-7268
-
(1998)
Phys Rev B
, vol.58
, pp. 7260-7268
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seifert, G.8
-
10
-
-
33646356998
-
Development of effective quantum mechanical/molecular mechanical (qm/mm) methods for complex biological processes
-
Riccardi D, Schaefer P, Yang Y, Yu H, Ghosh N, Prat-Resina X, Konig P, Li G, Xu D, Guo H, Elstner M, Cui Q (2006) Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 110:6458-6469
-
(2006)
J Phys Chem B
, vol.110
, pp. 6458-6469
-
-
Riccardi, D.1
Schaefer, P.2
Yang, Y.3
Yu, H.4
Ghosh, N.5
Prat-Resina, X.6
Konig, P.7
Li, G.8
Xu, D.9
Guo, H.10
Elstner, M.11
Cui, Q.12
-
13
-
-
0033246389
-
Linear scaling electronic structure methods
-
Goedecker S (1999) Linear scaling electronic structure methods. Rev Mod Phys 71:1085-1123
-
(1999)
Rev Mod Phys
, vol.71
, pp. 1085-1123
-
-
Goedecker, S.1
-
14
-
-
0011621942
-
Direct calculation of electrondensity in density-functional theory
-
YangW(1991) Direct calculation of electrondensity in density-functional theory. Phys Rev Lett 66:1438-1441
-
(1991)
Phys Rev Lett
, vol.66
, pp. 1438-1441
-
-
Yang, W.1
-
15
-
-
0043144732
-
A density-matrix divide-And-conquer approach for electronicstructure calculations of large molecules
-
Yang W, Lee T (1995) A density-matrix divide-And-conquer approach for electronicstructure calculations of large molecules. J Chem Phys 103:5674-5678
-
(1995)
J Chem Phys
, vol.103
, pp. 5674-5678
-
-
Yang, W.1
Lee, T.2
-
16
-
-
4143104515
-
Semiempirical molecular orbital calculations with linear system size scaling
-
Dixon S, Merz K (1996) Semiempirical molecular orbital calculations with linear system size scaling. J Chem Phys 104:6643-6649
-
(1996)
J Chem Phys
, vol.104
, pp. 6643-6649
-
-
Dixon, S.1
Merz, K.2
-
17
-
-
0000721543
-
Fragment molecular orbital method: An approximate computational method for large molecules
-
Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M (1999) Fragment molecular orbital method: an approximate computational method for large molecules. Chem Phys Lett 313:701-706
-
(1999)
Chem Phys Lett
, vol.313
, pp. 701-706
-
-
Kitaura, K.1
Ikeo, E.2
Asada, T.3
Nakano, T.4
Uebayasi, M.5
-
18
-
-
0037122848
-
Fragment molecular orbital method: Use of approximate electrostatic potential
-
Nakano T, Kaminuma T, Sato T, Fukuzawa K, Akiyama Y, Uebayasi M, Kitaura K (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
Uebayasi, M.6
Kitaura, K.7
-
19
-
-
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
-
20
-
-
4143088551
-
An efficient linear scaling method for ab initio calculation of electron density of proteins
-
Gao A, Zhang D, Zhang J, Zhang Y (2004) An efficient linear scaling method for ab initio calculation of electron density of proteins. Chem Phys Lett 394:293-297
-
(2004)
Chem Phys Lett
, vol.394
, pp. 293-297
-
-
Gao, A.1
Zhang, D.2
Zhang, J.3
Zhang, Y.4
-
21
-
-
22944470256
-
A new method for direct calculation of total energy of protein
-
He X, Zhang J (2005) A new method for direct calculation of total energy of protein. J Chem Phys 122:031103
-
(2005)
J Chem Phys
, vol.122
, pp. 031103
-
-
He, X.1
Zhang, J.2
-
22
-
-
0041377620
-
Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy
-
Zhang D, Zhang J (2003) Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J Chem Phys 119:3599-3605
-
(2003)
J Chem Phys
, vol.119
, pp. 3599-3605
-
-
Zhang, D.1
Zhang, J.2
-
23
-
-
77950180614
-
Multilevel fragment-based approach (mfba): A novel hybrid computational method for the study of large molecules
-
Rezac J, Salahub D (2010) Multilevel fragment-based approach (MFBA): a novel hybrid computational method for the study of large molecules. J Comp Theor Comput 6:91-99
-
(2010)
J Comp Theor Comput
, vol.6
, pp. 91-99
-
-
Rezac, J.1
Salahub, D.2
-
24
-
-
0001131626
-
Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations
-
Stewart J (1996) Application of localized molecular orbitals to the solution of semiempirical self-consistent field equations. Int J Quant Chem 58:133-146
-
(1996)
Int J Quant Chem
, vol.58
, pp. 133-146
-
-
Stewart, J.1
-
26
-
-
77950172747
-
Divide and conquer hartree-fock calculations on proteins
-
He X, Merz K (2010) Divide and conquer Hartree-Fock calculations on proteins. J Comp Theor Comput 6:405-411
-
(2010)
J Comp Theor Comput
, vol.6
, pp. 405-411
-
-
He, X.1
Merz, K.2
-
27
-
-
0000336097
-
Comparison of linearscaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions
-
Titmuss S, Cummins P, Bliznyuk A, Rendell A, Gready J (2000) Comparison of linearscaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions. Chem Phys Lett 320:169-176
-
(2000)
Chem Phys Lett
, vol.320
, pp. 169-176
-
-
Titmuss, S.1
Cummins, P.2
Bliznyuk, A.3
Rendell, A.4
Gready, J.5
-
28
-
-
85018193144
-
A guide to qm/mm methodology and applications
-
Zhang R, Lev B, Cuervo J, Noskov S, Salahub D (2010) A guide to QM/MM methodology and applications. Adv Quant Chem 59:353-400
-
(2010)
Adv Quant Chem
, vol.59
, pp. 353-400
-
-
Zhang, R.1
Lev, B.2
Cuervo, J.3
Noskov, S.4
Salahub, D.5
-
29
-
-
0038016725
-
Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies
-
Zhang Y, Kua J, McCammon J (2003) Influence of structural fluctuation on enzyme reaction energy barriers in combined quantum mechanical/molecular mechanical studies. J Phys Chem B 107:4459-4463
-
(2003)
J Phys Chem B
, vol.107
, pp. 4459-4463
-
-
Zhang, Y.1
Kua, J.2
McCammon, J.3
-
30
-
-
24344484047
-
On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions
-
Klahn M, Braun-Sand S, Rosta E, Warshel A (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J Phys Chem B 109:15645-15650
-
(2005)
J Phys Chem B
, vol.109
, pp. 15645-15650
-
-
Klahn, M.1
Braun-Sand, S.2
Rosta, E.3
Warshel, A.4
-
31
-
-
7044239742
-
Free-energy calculations -Applications to chemical and biochemical phenomena
-
Kollman P (1993) Free-energy calculations -Applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417
-
(1993)
Chem Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
32
-
-
77949273985
-
The application of quantum chemistry and condensed matter theory in studying amino-Acids, protein folding and anticancer drug technology
-
March N, Matthai C (2010) The application of quantum chemistry and condensed matter theory in studying amino-Acids, protein folding and anticancer drug technology. Theo Chem Acc 125:193-201
-
(2010)
Theo Chem Acc
, vol.125
, pp. 193-201
-
-
March, N.1
Matthai, C.2
-
33
-
-
10844239937
-
First-principles quantum chemistry in the life sciences
-
van Mourik T (2004) First-principles quantum chemistry in the life sciences. Phil Trans Royal Soc A 362:2653-2670
-
(2004)
Phil Trans Royal Soc A
, vol.362
, pp. 2653-2670
-
-
Van Mourik, T.1
-
34
-
-
0030745939
-
Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields
-
Beachy M, Chasman D, Murphy R, Halgren T, Friesner R (1997) Accurate ab initio quantum chemical determination of the relative energetics of peptide conformations and assessment of empirical force fields. J Am Chem Soc 119:5908-5920
-
(1997)
J Am Chem Soc
, vol.119
, pp. 5908-5920
-
-
Beachy, M.1
Chasman, D.2
Murphy, R.3
Halgren, T.4
Friesner, R.5
-
35
-
-
0035397197
-
Conformational dynamics of an alanine dipeptide analog: An ab initio molecular dynamics study
-
Wei D, Guo H, Salahub D (2001) Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study. Phys Rev E 64:011907
-
(2001)
Phys Rev E
, vol.64
, pp. 011907
-
-
Wei, D.1
Guo, H.2
Salahub, D.3
-
36
-
-
11644291455
-
Importance of correlation-gradient geometry optimization for molecular conformational-Analyses
-
Frey R, Coffin J, Newton S, Ramek M, Cheng V, Momany F, Schafer L (1992) Importance of correlation-gradient geometry optimization for molecular conformational-Analyses. J Am Chem Soc 114:5369-5377
-
(1992)
J Am Chem Soc
, vol.114
, pp. 5369-5377
-
-
Frey, R.1
Coffin, J.2
Newton, S.3
Ramek, M.4
Cheng, V.5
Momany, F.6
Schafer, L.7
-
37
-
-
0002634608
-
The case of glycine continued -some contradictory scf results
-
Ramek M, Cheng V, Frey R, Newton S, Schafer L (1991) The case of glycine continued -some contradictory SCF results. J Mol Struct Theochem 81:1-10
-
(1991)
J Mol Struct Theochem
, vol.81
, pp. 1-10
-
-
Ramek, M.1
Cheng, V.2
Frey, R.3
Newton, S.4
Schafer, L.5
-
38
-
-
31544437460
-
Ir study on stacking manner of peptide nanorings in peptide nanotubes
-
Nagai Y, Nakanishi T, Okamoto H, Takeda K, Furukawa Y, Usui K, Mihara H (2005) IR study on stacking manner of peptide nanorings in peptide nanotubes. Jpn J Appl Phys 44:7654-7661
-
(2005)
Jpn J Appl Phys
, vol.44
, pp. 7654-7661
-
-
Nagai, Y.1
Nakanishi, T.2
Okamoto, H.3
Takeda, K.4
Furukawa, Y.5
Usui, K.6
Mihara, H.7
-
39
-
-
0037444583
-
Vibrational absorption spectra, dft and scc-dftb conformational study and analysis of [leu]enkephalin
-
Abdali S, Niehaus T, Jalkanen K, Cao X, Nafie L, Frauenheim T, Suhai S, Bohr H (2003) Vibrational absorption spectra, DFT and SCC-DFTB conformational study and analysis of [Leu]enkephalin. Phys Chem Chem Phys 5:1295-1300
-
(2003)
Phys Chem Chem Phys
, vol.5
, pp. 1295-1300
-
-
Abdali, S.1
Niehaus, T.2
Jalkanen, K.3
Cao, X.4
Nafie, L.5
Frauenheim, T.6
Suhai, S.7
Bohr, H.8
-
40
-
-
33645106110
-
Use of vibrational spectroscopy to study protein and dna structure, hydration, and binding of biomolecules: A combined theoretical and experimental approach
-
Jalkanen K, Jurgensen V, Claussen A, Rahim A, Jensen G, Wade R, Nardi F, Jung C, Degtyarenko I, Nieminen R, Herrmann F, Knapp-Mohammady M, Niehaus T, Frimand K, Suhai S (2006) Use of vibrational spectroscopy to study protein and DNA structure, hydration, and binding of biomolecules: a combined theoretical and experimental approach. Int J Quant Chem 106:1160-1198
-
(2006)
Int J Quant Chem
, vol.106
, pp. 1160-1198
-
-
Jalkanen, K.1
Jurgensen, V.2
Claussen, A.3
Rahim, A.4
Jensen, G.5
Wade, R.6
Nardi, F.7
Jung, C.8
Degtyarenko, I.9
Nieminen, R.10
Herrmann, F.11
Knapp-Mohammady, M.12
Niehaus, T.13
Frimand, K.14
Suhai, S.15
-
41
-
-
0001167142
-
Transfer of molecular property tensors in cartesian coordinates: A new algorithm for simulation of vibrational spectra
-
Bour P, Sopkova J, Bednarova L, Malon P, Keiderling T (1997) Transfer of molecular property tensors in Cartesian coordinates: a new algorithm for simulation of vibrational spectra. J Comp Chem 18:646-659
-
(1997)
J Comp Chem
, vol.18
, pp. 646-659
-
-
Bour, P.1
Sopkova, J.2
Bednarova, L.3
Malon, P.4
Keiderling, T.5
-
42
-
-
0011083273
-
Harmonic vibrational frequencies: An evaluation of hartree-fock, moller-plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors
-
Scott A, Radom L (1996) Harmonic vibrational frequencies: an evaluation of Hartree-Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors. J Phys Chem 100:16502-16513
-
(1996)
J Phys Chem
, vol.100
, pp. 16502-16513
-
-
Scott, A.1
Radom, L.2
-
43
-
-
0030556776
-
N-Acetyl-l-Alanine n'-methylamide: A density functional analysis of the vibrational absorption and vibrational circular dichroism spectra
-
Jalkanen K, Suhai S (1996) N-Acetyl-L-Alanine N'-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra. Chem Phys 208:81-116
-
(1996)
Chem Phys
, vol.208
, pp. 81-116
-
-
Jalkanen, K.1
Suhai, S.2
-
44
-
-
0035814332
-
Differentiation of beta-sheet-forming structures: Ab initio-based simulations of ir absorption and vibrational cd for model peptide and protein beta-sheets
-
Kubelka J, Keiderling T (2001) Differentiation of beta-sheet-forming structures: ab initio-based simulations of IR absorption and vibrational CD for model peptide and protein beta-sheets. J Am Chem Soc 123:12048-12058
-
(2001)
J Am Chem Soc
, vol.123
, pp. 12048-12058
-
-
Kubelka, J.1
Keiderling, T.2
-
45
-
-
0037093868
-
Discrimination between peptide 3(10)-And alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra
-
Kubelka J, Silva R, Keiderling T (2002) Discrimination between peptide 3(10)-And alpha-helices. Theoretical analysis of the impact of alpha-methyl substitution on experimental spectra. J Am Chem Soc 124:5325-5332
-
(2002)
J Am Chem Soc
, vol.124
, pp. 5325-5332
-
-
Kubelka, J.1
Silva, R.2
Keiderling, T.3
-
46
-
-
18444365588
-
Solvent effects on ir and vcd spectra of helical peptides: Dft-based static spectral simulations with explicit water
-
Kubelka J, Huang R, Keiderling T (2005) Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water. J Phys Chem B 109:8231-8243
-
(2005)
J Phys Chem B
, vol.109
, pp. 8231-8243
-
-
Kubelka, J.1
Huang, R.2
Keiderling, T.3
-
47
-
-
0037111358
-
Discriminating 3(10)-from alpha helices: Vibrational and electronic cd and ir absorption study of related aib-containing oligopeptides
-
Silva R, Yasui S, Kubelka J, Formaggio F, Crisma M, Toniolo C, Keiderling T (2002) Discriminating 3(10)-from alpha helices: vibrational and electronic CD and IR absorption study of related Aib-containing oligopeptides. Biopolymers 65:229-243
-
(2002)
Biopolymers
, vol.65
, pp. 229-243
-
-
Silva, R.1
Yasui, S.2
Kubelka, J.3
Formaggio, F.4
Crisma, M.5
Toniolo, C.6
Keiderling, T.7
-
48
-
-
0037026869
-
Ab initio quantum mechanical models of peptide helices and their vibrational spectra
-
Bour P, Kubelka J, Keiderling T (2002) Ab initio quantum mechanical models of peptide helices and their vibrational spectra. Biopolymers 65:45-59
-
(2002)
Biopolymers
, vol.65
, pp. 45-59
-
-
Bour, P.1
Kubelka, J.2
Keiderling, T.3
-
49
-
-
84961981133
-
Empirical modeling of the peptide amide i band ir intensity in water solution
-
Bour P, Keiderling T (2003) Empirical modeling of the peptide amide I band IR intensity in water solution. J Chem Phys 119:11253-11262
-
(2003)
J Chem Phys
, vol.119
, pp. 11253-11262
-
-
Bour, P.1
Keiderling, T.2
-
50
-
-
2342487975
-
Structure, spectra and the effects of twisting of beta-sheet peptides. A density functional theory study
-
Bour P, Keiderling T (2004) Structure, spectra and the effects of twisting of beta-sheet peptides. A density functional theory study. J Mol Struct Theochem 675:95-105
-
(2004)
J Mol Struct Theochem
, vol.675
, pp. 95-105
-
-
Bour, P.1
Keiderling, T.2
-
51
-
-
30544437694
-
Vibrational spectral simulation for peptides of mixed secondary structure: Method comparisons with the trpzip model hairpin
-
Bour P, Keiderling T (2005) Vibrational spectral simulation for peptides of mixed secondary structure: method comparisons with the TrpZip model hairpin. J Phys Chem B 109:23687-23697
-
(2005)
J Phys Chem B
, vol.109
, pp. 23687-23697
-
-
Bour, P.1
Keiderling, T.2
-
52
-
-
0037434686
-
Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alpha-helices
-
Ireta J, Neugebauer J, Scheffler M, Rojo A, Galvan M (2003) Density functional theory study of the cooperativity of hydrogen bonds in finite and infinite alpha-helices. J Phys Chem B 107:1432-1437
-
(2003)
J Phys Chem B
, vol.107
, pp. 1432-1437
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
Rojo, A.4
Galvan, M.5
-
53
-
-
29044449043
-
Structural transitions in the polyalanine alpha-helix under uniaxial strain
-
Ireta J, Neugebauer J, Scheffler M, Rojo A, Galvan M (2005) Structural transitions in the polyalanine alpha-helix under uniaxial strain. J Am Chem Soc 127:17241-17244
-
(2005)
J Am Chem Soc
, vol.127
, pp. 17241-17244
-
-
Ireta, J.1
Neugebauer, J.2
Scheffler, M.3
Rojo, A.4
Galvan, M.5
-
54
-
-
69549091507
-
Density functional theory study of the conformational space of an infinitely long polypeptide chain
-
Ireta J, Scheffler M (2009) Density functional theory study of the conformational space of an infinitely long polypeptide chain. J Chem Phys 131:085104
-
(2009)
J Chem Phys
, vol.131
, pp. 085104
-
-
Ireta, J.1
Scheffler, M.2
-
55
-
-
27144463436
-
Enthalpies of hydrogen-bonds in alpha-helical peptides. An oniom dft/am1 study
-
Wieczorek R, Dannenberg J (2005) Enthalpies of hydrogen-bonds in alpha-helical peptides. An ONIOM DFT/AM1 study. J Am Chem Soc 127:14534-14535
-
(2005)
J Am Chem Soc
, vol.127
, pp. 14534-14535
-
-
Wieczorek, R.1
Dannenberg, J.2
-
56
-
-
34547252319
-
The effect of aqueous solvation upon alphahelix formation for polyalanines
-
Salvador P, Asensio A, Dannenberg JJ (2007) The effect of aqueous solvation upon alphahelix formation for polyalanines. J Phys Chem B 111:7462-7466
-
(2007)
J Phys Chem B
, vol.111
, pp. 7462-7466
-
-
Salvador, P.1
Asensio, A.2
Dannenberg, J.J.3
-
57
-
-
61749088371
-
Ramachandran revisited. Dft energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution
-
Tsai MIH, Xu Y, Dannenberg JJ (2009) Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution. J Phys Chem B 113:309-318
-
(2009)
J Phys Chem B
, vol.113
, pp. 309-318
-
-
Tsai, M.I.H.1
Xu, Y.2
Dannenberg, J.J.3
-
58
-
-
77249139740
-
The importance of hydrogen bonding between the glutamine side chains to the formation of amyloid vqivyk parallel beta-sheets: An oniom dft/am1 study
-
Plumley JA, Dannenberg JJ (2010) The importance of hydrogen bonding between the glutamine side chains to the formation of amyloid VQIVYK Parallel beta-sheets: an ONIOM DFT/AM1 Study. J Am Chem Soc 132:1758-1759
-
(2010)
J Am Chem Soc
, vol.132
, pp. 1758-1759
-
-
Plumley, J.A.1
Dannenberg, J.J.2
-
59
-
-
35948976959
-
Force field modeling of amino acid conformational energies
-
Kaminsky J, Jensen F (2007) Force field modeling of amino acid conformational energies. J Comp Theor Comput 3:1774-1788
-
(2007)
J Comp Theor Comput
, vol.3
, pp. 1774-1788
-
-
Kaminsky, J.1
Jensen, F.2
-
60
-
-
42649117457
-
Calculation of weakly polar interaction energies in polypeptides using density functional and local moller-plesset perturbation theory
-
Csontos J, Palermo N, Murphy R, Lovas S (2008) Calculation of weakly polar interaction energies in polypeptides using density functional and local Moller-Plesset perturbation theory. J Comp Chem 29:1344-1352
-
(2008)
J Comp Chem
, vol.29
, pp. 1344-1352
-
-
Csontos, J.1
Palermo, N.2
Murphy, R.3
Lovas, S.4
-
61
-
-
36048964831
-
Accurate ab initio study on the hydrogen-bond pairs in protein secondary structures
-
Wang ZWu C Lei H Duan Y (2007) Accurate ab initio study on the hydrogen-bond pairs in protein secondary structures. J Comp Theor Comput 3:1527-1537
-
(2007)
J Comp Theor Comput
, vol.3
, pp. 1527-1537
-
-
Wang, Z.1
Wu, C.2
Lei, H.3
Duan, Y.4
-
62
-
-
11644317783
-
Theoretical study of aqueous n-Acetyl-l-Alanine n '-methylamide: Structures and raman, vcd, and roa spectra
-
Han W, Jalkanen K, Elstner M, Suhai S (1998) Theoretical study of aqueous N-Acetyl-L-Alanine N '-methylamide: structures and Raman, VCD, and ROA spectra. J Phys Chem B 102:2587-2602
-
(1998)
J Phys Chem B
, vol.102
, pp. 2587-2602
-
-
Han, W.1
Jalkanen, K.2
Elstner, M.3
Suhai, S.4
-
63
-
-
39649124006
-
When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration
-
Thar J, Zahn S, Kirchner B (2008) When is a molecule properly solvated by a continuum model or in a cluster ansatz? a first-principles simulation of alanine hydration. J Phys Chem B 112:1456-1464
-
(2008)
J Phys Chem B
, vol.112
, pp. 1456-1464
-
-
Thar, J.1
Zahn, S.2
Kirchner, B.3
-
64
-
-
4043082766
-
Solvation model induced structural changes in peptides. A quantum chemical study on ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model
-
Hudaky I, Hudaky P, Perczel A (2004) Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model. J Comp Chem 25:1522-1531
-
(2004)
J Comp Chem
, vol.25
, pp. 1522-1531
-
-
Hudaky, I.1
Hudaky, P.2
Perczel, A.3
-
65
-
-
5544301524
-
Solvation effects on alanine dipeptide: A mp2/cc-pvtz//mp2/6-31 gstudy of (phi, psi) energy maps and conformers in the gas phase, ether, and water
-
Wang Z, Duan Y (2004) Solvation effects on alanine dipeptide: a MP2/cc-pVTZ//MP2/6-31Gstudy of (Phi, Psi) energy maps and conformers in the gas phase, ether, and water. J Comp Chem 25:1699-1716
-
(2004)
J Comp Chem
, vol.25
, pp. 1699-1716
-
-
Wang, Z.1
Duan, Y.2
-
66
-
-
77950565373
-
Multicanonical ab inito qm/mm molecular dynamics simulation of a peptide in an aqueous environment
-
Jono R, Watanabe Y, Shimizu K, Terada T (2010) Multicanonical ab Inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment. J Comp Chem 31:1168-1175
-
(2010)
J Comp Chem
, vol.31
, pp. 1168-1175
-
-
Jono, R.1
Watanabe, Y.2
Shimizu, K.3
Terada, T.4
-
67
-
-
40849105036
-
Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: Comparisons with ir and vibrational circular dichroism spectra
-
Kwac K, Lee K, Han J, Oh K, Cho M (2008) Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra. J Chem Phys 128:105106
-
(2008)
J Chem Phys
, vol.128
, pp. 105106
-
-
Kwac, K.1
Lee, K.2
Han, J.3
Oh, K.4
Cho, M.5
-
68
-
-
3543073498
-
Structures of the peptide-water complexes studied by the hybrid quantum mechanical-molecular mechanical (qm/mm) technique
-
Nemukhin A, Grigorenko B, Bochenkova A, Kovba V, Epifanovsky E (2004) Structures of the peptide-water complexes studied by the hybrid quantum mechanical-molecular mechanical (QM/MM) technique. Struct Chem 15:3-9
-
(2004)
Struct Chem
, vol.15
, pp. 3-9
-
-
Nemukhin, A.1
Grigorenko, B.2
Bochenkova, A.3
Kovba, V.4
Epifanovsky, E.5
-
69
-
-
0034225123
-
Hybrid scc-dftb/molecular mechanical studies of h-bonded systems and of n-Acetyl-(lala)(n) n '-methylamide helices in water solution
-
HanW, Elstner M, Jalkanen K, Frauenheim T, Suhai S (2000) Hybrid SCC-DFTB/molecular mechanical studies of H-bonded systems and of N-Acetyl-(L-Ala)(n) N '-methylamide helices in water solution. Int J Quant Chem 78:459-479
-
(2000)
Int J Quant Chem
, vol.78
, pp. 459-479
-
-
HanW Elstner, M.1
Jalkanen, K.2
Frauenheim, T.3
Suhai, S.4
-
70
-
-
33645317068
-
A comparative theoretical study of dipeptide solvation in water
-
Hugosson H, Laio A, Maurer P, Rothlisberger U (2006) A comparative theoretical study of dipeptide solvation in water. J Comp Chem 27:672-684
-
(2006)
J Comp Chem
, vol.27
, pp. 672-684
-
-
Hugosson, H.1
Laio, A.2
Maurer, P.3
Rothlisberger, U.4
-
71
-
-
34248337950
-
L-Alanine in a droplet of water: A density-functional molecular dynamics study
-
Degtyarenko I, Jalkanen K, Gurtovenko A, Nieminen R (2007) L-Alanine in a droplet of water: a density-functional molecular dynamics study. J Phys Chem B 111:4227-4234
-
(2007)
J Phys Chem B
, vol.111
, pp. 4227-4234
-
-
Degtyarenko, I.1
Jalkanen, K.2
Gurtovenko, A.3
Nieminen, R.4
-
72
-
-
2342576780
-
Amino acids and small peptides as building blocks for proteins: Comparative theoretical and spectroscopic studies
-
Jalkanen K, Elstner M, Suhai S (2004) Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies. J Mol Struct Theochem 675:61-77
-
(2004)
J Mol Struct Theochem
, vol.675
, pp. 61-77
-
-
Jalkanen, K.1
Elstner, M.2
Suhai, S.3
-
73
-
-
37549015952
-
Role of hydration in determining the structure andvibrational spectraof l-Alanine andn-Acetyl l-Alaninen'-methylamide in aqueous solution: A combined theoretical and experimental approach
-
Jalkanen KJ, Degtyarenko IM, Nieminen RM, Cao X, Nafie LA, Zhu F, Barron LD (2008) Role of hydration in determining the structure andvibrational spectraof L-Alanine andN-Acetyl L-AlanineN'-methylamide in aqueous solution: a combined theoretical and experimental approach. Theor Chem Acc 119:191-210
-
(2008)
Theor Chem Acc
, vol.119
, pp. 191-210
-
-
Jalkanen, K.J.1
Degtyarenko, I.M.2
Nieminen, R.M.3
Cao, X.4
Nafie, L.A.5
Zhu, F.6
Barron, L.D.7
-
74
-
-
67651230424
-
Unravelling the conformational dynamics of the aqueous alanine dipeptide with first-principle molecular dynamics
-
GaigeotM(2009) Unravelling the conformational dynamics of the aqueous alanine dipeptide with first-principle molecular dynamics. J Phys Chem B 113:10059-10062
-
(2009)
J Phys Chem B
, vol.113
, pp. 10059-10062
-
-
Gaigeot, M.1
-
75
-
-
5244228724
-
Theoretical-study of blocked glycine and alanine peptide analogs
-
Headgordon T, Headgordon M, Frisch M, Brooks C, Pople J (1991) Theoretical-study of blocked glycine and alanine peptide analogs. J Am Chem Soc 113:5989-5997
-
(1991)
J Am Chem Soc
, vol.113
, pp. 5989-5997
-
-
Headgordon, T.1
Headgordon, M.2
Frisch, M.3
Brooks, C.4
Pople, J.5
-
76
-
-
0006279673
-
Solutionphase conformations of n-Acetyl-n'-methyl-l-Alaninamide from vibrational raman optical activity
-
Deng Z, Polavarapu P, Ford S, Hecht L, Barron L, Ewig C, Jalkanen K (1996) Solutionphase conformations of N-Acetyl-N'-methyl-L-Alaninamide from vibrational Raman optical activity. J Phys Chem 100:2025-2034
-
(1996)
J Phys Chem
, vol.100
, pp. 2025-2034
-
-
Deng, Z.1
Polavarapu, P.2
Ford, S.3
Hecht, L.4
Barron, L.5
Ewig, C.6
Jalkanen, K.7
-
77
-
-
84962448847
-
Conformation dynamics in peptides -quantumchemical calculations and molecular-dynamics simulations on n-Acetylalanyl-n'-methylamide
-
Rommelmohle K, Hofmann H (1993) Conformation dynamics in peptides -quantumchemical calculations and molecular-dynamics simulations on N-Acetylalanyl-N'-methylamide. J Mol Struct Theochem 104:211-219
-
(1993)
J Mol Struct Theochem
, vol.104
, pp. 211-219
-
-
Rommelmohle, K.1
Hofmann, H.2
-
78
-
-
0034656826
-
Dft studies on helix formation in n-Acetyl-(l-Alanyl) (n)-n '-methylamide for n1-20
-
Elstner M, Jalkanen K, Knapp-Mohammady M, Frauenheim T, Suhai S (2000) DFT studies on helix formation in N-Acetyl-(L-Alanyl) (n)-N '-methylamide for n1-20. Chem Phys 256:15-27
-
(2000)
Chem Phys
, vol.256
, pp. 15-27
-
-
Elstner, M.1
Jalkanen, K.2
Knapp-Mohammady, M.3
Frauenheim, T.4
Suhai, S.5
-
79
-
-
0035871701
-
Description of peptide and protein secondary structures employing semiempirical methods
-
Mohle K, Hofmann H, Thiel W (2001) Description of peptide and protein secondary structures employing semiempirical methods. J Comp Chem 22:509-520
-
(2001)
J Comp Chem
, vol.22
, pp. 509-520
-
-
Mohle, K.1
Hofmann, H.2
Thiel, W.3
-
80
-
-
0035863003
-
Energetics and structure of glycine and alanine based model peptides: Approximate scc-dftb, am1 and pm3 methods in comparison with dft, hf and mp2 calculations
-
Elstner M, Jalkanen K, Knapp-Mohammady M, Frauenheim T, Suhai S (2001) Energetics and structure of glycine and alanine based model peptides: approximate SCC-DFTB, AM1 and PM3 methods in comparison with DFT, HF and MP2 calculations. Chem Phys 263:203-219
-
(2001)
Chem Phys
, vol.263
, pp. 203-219
-
-
Elstner, M.1
Jalkanen, K.2
Knapp-Mohammady, M.3
Frauenheim, T.4
Suhai, S.5
-
81
-
-
0037441479
-
Comparison of a qm/mm force field and molecular mechanics force fields in simulations of alanine and glycine dipeptides" (ace-Ala-nme and ace-gly-nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
-
Hu H, Elstner M, Hermans J (2003) Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Protein Struct Funct Genet 50:451-463
-
(2003)
Protein Struct Funct Genet
, vol.50
, pp. 451-463
-
-
Hu, H.1
Elstner, M.2
Hermans, J.3
-
82
-
-
34547511107
-
Implementation of the scc-dftb method for hybrid qm/mm simulations within the amber molecular dynamics package
-
Seabra G, Walker R, Elstner M, Case D, Roitberg A (2007) Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A 111:5655-5664
-
(2007)
J Phys Chem A
, vol.111
, pp. 5655-5664
-
-
Seabra, G.1
Walker, R.2
Elstner, M.3
Case, D.4
Roitberg, A.5
-
83
-
-
46449105513
-
A versatile ambergaussian qm/mm interface through pupil
-
Torras J, Seabra G, Deumens E, Trickey S, Roitberg A (2008) A versatile AMBERGaussian QM/MM interface through PUPIL. J Comp Chem 29:1564-1573
-
(2008)
J Comp Chem
, vol.29
, pp. 1564-1573
-
-
Torras, J.1
Seabra, G.2
Deumens, E.3
Trickey, S.4
Roitberg, A.5
-
84
-
-
0242558240
-
An approximate dft method for qm/mm simulations of biological structures and processes
-
Elstner M, Frauenheim T, Suhai S (2003) An approximate DFT method for QM/MM simulations of biological structures and processes. J Mol Struct Theochem 632:29-41
-
(2003)
J Mol Struct Theochem
, vol.632
, pp. 29-41
-
-
Elstner, M.1
Frauenheim, T.2
Suhai, S.3
-
85
-
-
0037023160
-
A qm/mm approach with effective fragment potentials applied to the dipeptide-water structures
-
Nemukhin A, Grigorenko B, Bochenkova A, Topol I, Burt S (2002) A QM/MM approach with effective fragment potentials applied to the dipeptide-water structures. J Mol Struct Theochem 581:167-175
-
(2002)
J Mol Struct Theochem
, vol.581
, pp. 167-175
-
-
Nemukhin, A.1
Grigorenko, B.2
Bochenkova, A.3
Topol, I.4
Burt, S.5
-
86
-
-
0033633272
-
A self-consistent charge density-functional based tight-binding scheme for large biomolecules
-
Elstner M, Frauenheim T, Kaxiras E, Seifert G, Suhai S (2000) A self-consistent charge density-functional based tight-binding scheme for large biomolecules. Phys Stat Sol B 217:357-376
-
(2000)
Phys Stat Sol B
, vol.217
, pp. 357-376
-
-
Elstner, M.1
Frauenheim, T.2
Kaxiras, E.3
Seifert, G.4
Suhai, S.5
-
87
-
-
70350391878
-
Are current semiempirical methods better than force fields? A study from the thermodynamics perspective
-
Seabra G, Walker R, Roitberg A (2009) Are current semiempirical methods better than force fields? a study from the thermodynamics perspective. J PhysChemA 113:11938-11948
-
(2009)
J PhysChemA
, vol.113
, pp. 11938-11948
-
-
Seabra, G.1
Walker, R.2
Roitberg, A.3
-
88
-
-
44449137050
-
Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in rhf and mp2 with pople split-valence basis sets
-
Echenique P, Alonso J (2008) Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split-valence basis sets. J Comp Chem 29:1408-1422
-
(2008)
J Comp Chem
, vol.29
, pp. 1408-1422
-
-
Echenique, P.1
Alonso, J.2
-
89
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Protein Struct Funct Genet 65:712-725
-
(2006)
Protein Struct Funct Genet
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
90
-
-
33751287745
-
Conformational preferences of non-prolyl and prolyl residues
-
Kang Y (2006) Conformational preferences of non-prolyl and prolyl residues. J Phys Chem B 110:21338-21348
-
(2006)
J Phys Chem B
, vol.110
, pp. 21338-21348
-
-
Kang, Y.1
-
91
-
-
33751001006
-
First-principle studies of gaseous aromatic amino acid histidine
-
Huang Z, Yu W, Lin Z (2006) First-principle studies of gaseous aromatic amino acid histidine. J Mol Struct Theochem 801:7-20
-
(2006)
J Mol Struct Theochem
, vol.801
, pp. 7-20
-
-
Huang, Z.1
Yu, W.2
Lin, Z.3
-
92
-
-
75149112566
-
Computational study of hydrogen-bonding complex formation of helical polypeptides with water molecule
-
Makshakova O, Ermakova E (2010) Computational study of hydrogen-bonding complex formation of helical polypeptides with water molecule. J Mol Struct Theochem 942:7-14
-
(2010)
J Mol Struct Theochem
, vol.942
, pp. 7-14
-
-
Makshakova, O.1
Ermakova, E.2
-
93
-
-
2642585833
-
Importance of van der Waals interactions in QM/MM Simulations.
-
Riccardi D, Li G, Cui Q (2004) Importance of van der Waals interactions in QM/MM Simulations. J Phys Chem B 108:6467-6478
-
(2004)
J Phys Chem B
, vol.108
, pp. 6467-6478
-
-
Riccardi, D.1
Li, G.2
Cui, Q.3
-
94
-
-
43449103082
-
Benchmark database on isolated small peptides containing an aromatic side chain: Comparison between wave function and density functional theory methods and empirical force field
-
Valdes H, Pluhackova K, Pitonak M, Rezac J, Hobza P (2008) Benchmark database on isolated small peptides containing an aromatic side chain: comparison between wave function and density functional theory methods and empirical force field. Phys Chem Chem Phys 10:2747-2757
-
(2008)
Phys Chem Chem Phys
, vol.10
, pp. 2747-2757
-
-
Valdes, H.1
Pluhackova, K.2
Pitonak, M.3
Rezac, J.4
Hobza, P.5
-
95
-
-
53849094468
-
Potential-energy and free-energy surfaces of glycyl-phenylalanyl-Alanine (gfa) tripeptide: Experiment and theory
-
Valdes H, Spiwok V, Rezac J, Reha D, Abo-Riziq A, de Vries M, Hobza P (2008) Potential-energy and free-energy surfaces of glycyl-phenylalanyl-Alanine (GFA) tripeptide: experiment and theory. Chemistry Eur J 14:4886-4898
-
(2008)
Chemistry Eur J
, vol.14
, pp. 4886-4898
-
-
Valdes, H.1
Spiwok, V.2
Rezac, J.3
Reha, D.4
Abo-Riziq, A.5
De Vries, M.6
Hobza, P.7
-
96
-
-
73349129704
-
Phenylalanyl-glycyl-phenylalanine tripeptide: a model system for aromatic-Aromatic side chain interactions in proteins.
-
Valdes H, Pluhackova K, Hobza P (2009) Phenylalanyl-glycyl-phenylalanine tripeptide: a model system for aromatic-Aromatic side chain interactions in proteins. J Comp Theor Comput 5:2248-2256
-
(2009)
J Comp Theor Comput
, vol.5
, pp. 2248-2256
-
-
Valdes, H.1
Pluhackova, K.2
Hobza, P.3
-
97
-
-
75249094301
-
Fluoroolefins as peptidie mimetics. 2. A computational study of the conformational ramifications of peptide bond replacement
-
McKinney B, Urban J (2010) Fluoroolefins as peptidie mimetics. 2. A computational study of the conformational ramifications of peptide bond replacement. J Phys Chem A 114:1123-1133
-
(2010)
J Phys Chem A
, vol.114
, pp. 1123-1133
-
-
McKinney, B.1
Urban, J.2
-
98
-
-
36048981812
-
Establishing effective simulation protocols for beta-And alpha/beta-mixed peptides. I. Qm and qm/mm models
-
Zhu X, Yethiraj A, Cui Q (2007) Establishing effective simulation protocols for beta-And alpha/beta-mixed peptides. I. QM and QM/MM models. J Comp Theor Comput 3:1538-1549
-
(2007)
J Comp Theor Comput
, vol.3
, pp. 1538-1549
-
-
Zhu, X.1
Yethiraj, A.2
Cui, Q.3
-
99
-
-
0017100947
-
Theoretical studies of enzymic reactions -dielectric, electrostatic and steric stabilization of carboniumion in reaction of lysozyme
-
Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions -dielectric, electrostatic and steric stabilization of carboniumion in reaction of lysozyme. J Mol Biol 103:227-249
-
(1976)
J Mol Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
100
-
-
84986513644
-
A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
-
Field M, Bash P, Karplus M (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J Comp Chem 11:700-733
-
(1990)
J Comp Chem
, vol.11
, pp. 700-733
-
-
Field, M.1
Bash, P.2
Karplus, M.3
-
101
-
-
0027125907
-
A priori evaluation of aqueous polarization effects through monte-carlo qm-mm simulations
-
Gao J, Xia X (1992) A priori evaluation of aqueous polarization effects through monte-carlo QM-MM simulations. Science 258:631-635
-
(1992)
Science
, vol.258
, pp. 631-635
-
-
Gao, J.1
Xia, X.2
-
102
-
-
84962477148
-
Structure/function correlations of proteins using mm,qm/mm, and related approaches: Methods, concepts, pitfalls, and current progress
-
Shurki A, Warshel A (2003) Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress. Protein Sim 66:249-313
-
(2003)
Protein Sim
, vol.66
, pp. 249-313
-
-
Shurki, A.1
Warshel, A.2
-
103
-
-
31344459010
-
Quantum chemical studies of protein structure
-
Oldfield E (2005) Quantum chemical studies of protein structure. Phil Trans Royal Soc B 360:1347-1361
-
(2005)
Phil Trans Royal Soc B
, vol.360
, pp. 1347-1361
-
-
Oldfield, E.1
-
104
-
-
34547507515
-
Qm/mm methods for biological systems
-
Senn H, Thiel W (2007) QM/MM methods for biological systems. Top Curr Chem 268:173-290
-
(2007)
Top Curr Chem
, vol.268
, pp. 173-290
-
-
Senn, H.1
Thiel, W.2
-
105
-
-
0036286854
-
The role and perspective of a initio molecular dynamics in the study of biological systems
-
Carloni P, Rothlisberger U, Parrinello M (2002) The role and perspective of a initio molecular dynamics in the study of biological systems. Acc Chem Res 35:455-464
-
(2002)
Acc Chem Res
, vol.35
, pp. 455-464
-
-
Carloni, P.1
Rothlisberger, U.2
Parrinello, M.3
-
106
-
-
0010259404
-
Linear scaling computation of the fock matrix
-
Challacombe M, Schwegler E (1997) Linear scaling computation of the Fock matrix. J Chem Phys 106:5526-5536
-
(1997)
J Chem Phys
, vol.106
, pp. 5526-5536
-
-
Challacombe, M.1
Schwegler, E.2
-
107
-
-
0001166146
-
Ab initio geometry determinations of proteins. 1. Crambin
-
Van Alsenoy C, Yu C, Peeters A, Martin J, Schafer L (1998) Ab initio geometry determinations of proteins. 1. Crambin. J Phys Chem A 102:2246-2251
-
(1998)
J Phys Chem A
, vol.102
, pp. 2246-2251
-
-
Van Alsenoy, C.1
Yu, C.2
Peeters, A.3
Martin, J.4
Schafer, L.5
-
108
-
-
0000089238
-
Linear scaling density functional calculations with gaussian orbitals
-
Scuseria G (1999) Linear scaling density functional calculations with Gaussian orbitals. J Phys Chem A 103:4782-4790
-
(1999)
J Phys Chem A
, vol.103
, pp. 4782-4790
-
-
Scuseria, G.1
-
109
-
-
0035892820
-
Ab initio mo studies of interaction mechanisms of protein kinase c with cell membranes
-
Tsuda K, Kaneko H, Shimada J, Takada T (2001) Ab initio MO studies of interaction mechanisms of Protein Kinase C with cell membranes. Comp Phys Comm 142:140-143
-
(2001)
Comp Phys Comm
, vol.142
, pp. 140-143
-
-
Tsuda, K.1
Kaneko, H.2
Shimada, J.3
Takada, T.4
-
110
-
-
0000880259
-
Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory
-
Sato F, Yoshihiro T, Era M, Kashiwagi H (2001) Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory. Chem Phys Lett 341:645-651
-
(2001)
Chem Phys Lett
, vol.341
, pp. 645-651
-
-
Sato, F.1
Yoshihiro, T.2
Era, M.3
Kashiwagi, H.4
-
111
-
-
23044464749
-
All-electron density functional calculation on insulin with quasi-canonical localized orbitals
-
Inaba T, Tahara S, Nisikawa N, Kashiwagi H, Sato F (2005) All-electron density functional calculation on insulin with quasi-canonical localized orbitals. J Comp Chem 26:987-993
-
(2005)
J Comp Chem
, vol.26
, pp. 987-993
-
-
Inaba, T.1
Tahara, S.2
Nisikawa, N.3
Kashiwagi, H.4
Sato, F.5
-
112
-
-
34249884543
-
Molecular recognition mechanism of fk506 binding protein: An all-electron fragment molecular orbital study
-
Nakanishi I, Fedorov D, Kitaura K (2007) Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study. Protein Struct Funct Genet 68:145-158
-
(2007)
Protein Struct Funct Genet
, vol.68
, pp. 145-158
-
-
Nakanishi, I.1
Fedorov, D.2
Kitaura, K.3
-
113
-
-
33846226036
-
Density functional calculation of the electronic structure on insulin hexamer
-
Inaba T, Tsunekawa N, Hirano T, Yoshihiro T, Kashiwagi H, Sato F (2007) Density functional calculation of the electronic structure on insulin hexamer. Chem Phys Lett 434:331-335
-
(2007)
Chem Phys Lett
, vol.434
, pp. 331-335
-
-
Inaba, T.1
Tsunekawa, N.2
Hirano, T.3
Yoshihiro, T.4
Kashiwagi, H.5
Sato, F.6
-
114
-
-
21644468546
-
Insights into the interplay between electronic structure and protein dynamics: The case of ubiquitin
-
Pichierri F (2005) Insights into the interplay between electronic structure and protein dynamics: the case of ubiquitin. Chem Phys Lett 410:462-466
-
(2005)
Chem Phys Lett
, vol.410
, pp. 462-466
-
-
Pichierri, F.1
-
115
-
-
0242411480
-
Abinitioquality properties for macromolecules using the adma approach
-
ExnerT,MezeyP(2003)Abinitioquality properties for macromolecules using the ADMA approach. J Comp Chem 24:1980-1986
-
(2003)
J Comp Chem
, vol.24
, pp. 1980-1986
-
-
Exner, T.1
Mezey, P.2
-
116
-
-
84962467100
-
Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the poisson-boltzmann equation
-
Gogonea V, Merz K (1999) Fully quantum mechanical description of proteins in solution. Combining linear scaling quantum mechanical methodologies with the Poisson-Boltzmann equation. J Phys Chem A 103:5171-5188
-
(1999)
J Phys Chem A
, vol.103
, pp. 5171-5188
-
-
Gogonea, V.1
Merz, K.2
-
117
-
-
0343725680
-
Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems
-
van der Vaart A, Suarez D, Merz K (2000) Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems. J Chem Phys 113:10512-10523
-
(2000)
J Chem Phys
, vol.113
, pp. 10512-10523
-
-
Van Der Vaart, A.1
Suarez, D.2
Merz, K.3
-
118
-
-
0001499720
-
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
-
Van der Vaart A, Gogonea V, Dixon S, Merz K (2000) Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J Comp Chem 21:1494-1504
-
(2000)
J Comp Chem
, vol.21
, pp. 1494-1504
-
-
Van Der Vaart, A.1
Gogonea, V.2
Dixon, S.3
Merz, K.4
-
119
-
-
4043173012
-
Full ab initio computation of protein-water interaction energies
-
Zhang D, Zhang J (2004) Full ab initio computation of protein-water interaction energies. J Theor Comp Chem 3:43-49
-
(2004)
J Theor Comp Chem
, vol.3
, pp. 43-49
-
-
Zhang, D.1
Zhang, J.2
-
120
-
-
0346506503
-
Fast, accurate semiempirical molecular orbital calculations for macromolecules
-
Dixon S, Merz K (1997) Fast, accurate semiempirical molecular orbital calculations for macromolecules. J Chem Phys 107:879-893
-
(1997)
J Chem Phys
, vol.107
, pp. 879-893
-
-
Dixon, S.1
Merz, K.2
-
121
-
-
33748283200
-
The scc-dftb method and its application to biological systems
-
Elstner M (2006) The SCC-DFTB method and its application to biological systems. Theo Chem Acc 116:316-325
-
(2006)
Theo Chem Acc
, vol.116
, pp. 316-325
-
-
Elstner, M.1
-
122
-
-
0035451906
-
Quantum mechanics simulation of protein dynamics on long timescale
-
Liu H, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W (2001) Quantum mechanics simulation of protein dynamics on long timescale. Protein Struct Funct Genet 44:484-489
-
(2001)
Protein Struct Funct Genet
, vol.44
, pp. 484-489
-
-
Liu, H.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Hermans, J.5
Yang, W.6
-
123
-
-
79952608525
-
Accurate bond and angle parameters for x-ray protein-structure refinement
-
Engh R, Huber R (1991) Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Cryst A 47:392-400
-
(1991)
Acta Cryst A
, vol.47
, pp. 392-400
-
-
Engh, R.1
Huber, R.2
-
124
-
-
24044522903
-
Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics
-
Yu N, Yennawar H, Merz K (2005) Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. Acta Cryst D 61:322-332
-
(2005)
Acta Cryst D
, vol.61
, pp. 322-332
-
-
Yu, N.1
Yennawar, H.2
Merz, K.3
-
125
-
-
33751517368
-
Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement
-
Yu N, Li X, Cui G, Hayik S, Merz K (2006) Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Prot Sc 15:2773-2784
-
(2006)
Prot Sc
, vol.15
, pp. 2773-2784
-
-
Yu, N.1
Li, X.2
Cui, G.3
Hayik, S.4
Merz, K.5
-
126
-
-
33748341319
-
Density-functional geometry optimization of the 150 000-Atom photosystem-i trimer
-
Canfield P, Dahlbom M, Hush N, Reimers J (2006) Density-functional geometry optimization of the 150 000-Atom photosystem-I trimer. J Chem Phys 124:024301
-
(2006)
J Chem Phys
, vol.124
, pp. 024301
-
-
Canfield, P.1
Dahlbom, M.2
Hush, N.3
Reimers, J.4
-
127
-
-
67349218843
-
Application of the pm6 method to modeling proteins
-
Stewart J (2009) Application of the PM6 method to modeling proteins. J Mol Model 15:765-805
-
(2009)
J Mol Model
, vol.15
, pp. 765-805
-
-
Stewart, J.1
-
128
-
-
36048967855
-
Assessment of semiempirical quantum mechanical methods for the evaluation of protein structures
-
Wollacott A, Merz K (2007) Assessment of semiempirical quantum mechanical methods for the evaluation of protein structures. J Comp Theor Comput 3:1609-1619
-
(2007)
J Comp Theor Comput
, vol.3
, pp. 1609-1619
-
-
Wollacott, A.1
Merz, K.2
-
129
-
-
65249103328
-
Importance of dispersion and electron correlation in ab initio protein folding
-
He X, Fusti-Molnar L, Cui G, Merz K (2009) Importance of Dispersion and Electron Correlation in ab Initio Protein Folding. J Phys Chem B 113:5290-5300
-
(2009)
J Phys Chem B
, vol.113
, pp. 5290-5300
-
-
He, X.1
Fusti-Molnar, L.2
Cui, G.3
Merz, K.4
-
130
-
-
3042547956
-
Comparison of quantum mechanics and molecular mechanics dimerization energy landscapes for pairs of ring-containing amino acids in proteins
-
Morozov A, Misura K, Tsemekhman K, Baker D (2004) Comparison of quantum mechanics and molecular mechanics dimerization energy landscapes for pairs of ring-containing amino acids in proteins. J Phys Chem B 108:8489-8496
-
(2004)
J Phys Chem B
, vol.108
, pp. 8489-8496
-
-
Morozov, A.1
Misura, K.2
Tsemekhman, K.3
Baker, D.4
-
131
-
-
43949093801
-
Ab initio based polarizable force field parametrization
-
Masia M (2008) Ab initio based polarizable force field parametrization. J Chem Phys 128:184107
-
(2008)
J Chem Phys
, vol.128
, pp. 184107
-
-
Masia, M.1
-
132
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell A, Feig M, Brooks C (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comp Chem 25:1400-1415
-
(2004)
J Comp Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell, A.1
Feig, M.2
Brooks, C.3
-
133
-
-
57749085330
-
Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. Ii. Towards an improvement of force fields used for classical molecular dynamics simulations
-
Okiyama Y, Watanabe H, Fukuzawa K, Nakano T, Mochizuki Y, Ishikawa T, Ebina K, Tanaka S (2009) Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations. Chem Phys Lett 467:417-423
-
(2009)
Chem Phys Lett
, vol.467
, pp. 417-423
-
-
Okiyama, Y.1
Watanabe, H.2
Fukuzawa, K.3
Nakano, T.4
Mochizuki, Y.5
Ishikawa, T.6
Ebina, K.7
Tanaka, S.8
-
135
-
-
77954566051
-
The red. Tools: Advances in resp and esp charge derivation and force field library building
-
Dupradeau F, Pigache A, Zaffran T, Savineau C, Lelong R, Grivel N, Lelong D, Rosanski W, Cieplak P (2010) The R.ED. tools: advances in RESP and ESP charge derivation and force field library building. Phys Chem Chem Phys 12:7821-7839
-
(2010)
Phys Chem Chem Phys
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
136
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan Y, Wu C, Chowdhury S, Lee M, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comp Chem 24:1999-2012
-
(2003)
J Comp Chem
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
137
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges -The resp model
-
Bayly C, Cieplak P, Cornell W, Kollman P (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges -the RESP model. J Phys Chem 97:10269-10280
-
(1993)
J Phys Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.1
Cieplak, P.2
Cornell, W.3
Kollman, P.4
-
138
-
-
0037173897
-
D-resp: Dynamically generated electrostatic potential derived charges from quantum mechanics/molecular mechanics simulations
-
Laio A, VandeVondele J, Rothlisberger U (2002) D-RESP: dynamically generated electrostatic potential derived charges from quantum mechanics/molecular mechanics simulations. J Phys Chem B 106:7300-7307
-
(2002)
J Phys Chem B
, vol.106
, pp. 7300-7307
-
-
Laio, A.1
VandeVondele, J.2
Rothlisberger, U.3
-
139
-
-
84940492598
-
Interatomic potentials from 1st-principles calculations -The force-matching method
-
Ercolessi F, Adams J (1994) Interatomic potentials from 1st-principles calculations -the force-matching method. Europhys Lett 26:583-588
-
(1994)
Europhys Lett
, vol.26
, pp. 583-588
-
-
Ercolessi, F.1
Adams, J.2
-
140
-
-
0034635566
-
Physics of iron at earth's core conditions
-
Laio A, Bernard S, Chiarotti G, Scandolo S, Tosatti E (2000) Physics of iron at Earth's core conditions. Science 287:1027-1030
-
(2000)
Science
, vol.287
, pp. 1027-1030
-
-
Laio, A.1
Bernard, S.2
Chiarotti, G.3
Scandolo, S.4
Tosatti, E.5
-
141
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
-
Izvekov S, Parrinello M, Burnham C, Voth G (2004) Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J Chem Phys 120:10896-10913
-
(2004)
J Chem Phys
, vol.120
, pp. 10896-10913
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.3
Voth, G.4
-
142
-
-
49749128815
-
Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method
-
Akin-Ojo O, Song Y, Wang F (2008) Developing ab initio quality force fields from condensed phase quantum-mechanics/molecular-mechanics calculations through the adaptive force matching method. J Chem Phys 129:064108
-
(2008)
J Chem Phys
, vol.129
, pp. 064108
-
-
Akin-Ojo, O.1
Song, Y.2
Wang, F.3
-
143
-
-
34147116967
-
Automated parametrization of biomolecular force fields from quantum mechanics/molecular mechanics (qm/mm) simulations through force matching
-
Maurer P, Laio A, Hugosson H, Colombo M, Rothlisberger U (2007) Automated parametrization of biomolecular force fields from quantum mechanics/molecular mechanics (QM/MM) simulations through force matching. J Comp Theor Comput 3:628-639
-
(2007)
J Comp Theor Comput
, vol.3
, pp. 628-639
-
-
Maurer, P.1
Laio, A.2
Hugosson, H.3
Colombo, M.4
Rothlisberger, U.5
-
144
-
-
73549112903
-
Developing improved charge sets for the modeling of the kcsa k+ channel using qm/mm electrostatic potentials
-
Bucher D, Guidoni L, Maurer P, Rothlisberger U (2009) Developing improved charge sets for the modeling of the KcsA K+ channel using QM/MM electrostatic potentials. J Comp Theor Comput 5:2173-2179
-
(2009)
J Comp Theor Comput
, vol.5
, pp. 2173-2179
-
-
Bucher, D.1
Guidoni, L.2
Maurer, P.3
Rothlisberger, U.4
-
145
-
-
77953029106
-
Molecular simulations of ion channels: A quantum chemist's perspective
-
Bucher D, Rothlisberger U (2010) Molecular simulations of ion channels: a quantum chemist's perspective. J Gener Phys 135:549-554
-
(2010)
J Gener Phys
, vol.135
, pp. 549-554
-
-
Bucher, D.1
Rothlisberger, U.2
-
146
-
-
0034292649
-
Microscopic model of carbon monoxide binding to myoglobin
-
McMahon B, Stojkovic B, Hay P, Martin R, Garcia A (2000) Microscopic model of carbon monoxide binding to myoglobin. J Chem Phys 113:6831-6850
-
(2000)
J Chem Phys
, vol.113
, pp. 6831-6850
-
-
McMahon, B.1
Stojkovic, B.2
Hay, P.3
Martin, R.4
Garcia, A.5
-
147
-
-
33646497457
-
Dioxygen affinity in heme proteins investigated by computer simulation
-
Marti M, Crespo A, Capece L, Boechi L, Bikiel D, Scherlis D, Estrin D (2006) Dioxygen affinity in heme proteins investigated by computer simulation. J Inorg Biochem 100:761-770
-
(2006)
J Inorg Biochem
, vol.100
, pp. 761-770
-
-
Marti, M.1
Crespo, A.2
Capece, L.3
Boechi, L.4
Bikiel, D.5
Scherlis, D.6
Estrin, D.7
-
148
-
-
0038369961
-
How iron-containing proteins control dioxygen chemistry: A detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations
-
Friesner R, Baik M, Gherman B, Guallar V, Wirstam M, Murphy R, Lippard S (2003) How iron-containing proteins control dioxygen chemistry: a detailed atomic level description via accurate quantum chemical and mixed quantum mechanics/molecular mechanics calculations. Coord Chem Rev 238:267-290
-
(2003)
Coord Chem Rev
, vol.238
, pp. 267-290
-
-
Friesner, R.1
Baik, M.2
Gherman, B.3
Guallar, V.4
Wirstam, M.5
Murphy, R.6
Lippard, S.7
-
149
-
-
52349112004
-
Exploring the interstitial atom in the femo cofactor of nitrogenase: Insights from qm and qm/mm calculations
-
Xie H, Wu R, Zhou Z, Cao Z (2008) Exploring the interstitial atom in the FeMo cofactor of nitrogenase: insights from QM and QM/MM calculations. J Phys Chem B 112:11435-11439
-
(2008)
J Phys Chem B
, vol.112
, pp. 11435-11439
-
-
Xie, H.1
Wu, R.2
Zhou, Z.3
Cao, Z.4
-
150
-
-
67651213773
-
Polarization effects stabilize bacteriorhodopsin's chromophore binding pocket: A molecular dynamics study
-
BabitzkiG,DenschlagR,TavanP(2009)Polarization effects stabilize Bacteriorhodopsin's chromophore binding pocket: a molecular dynamics study. J Phys Chem B 113:10483-10495
-
(2009)
J Phys Chem B
, vol.113
, pp. 10483-10495
-
-
Babitzki, G.1
Denschlag, R.2
Tavan, P.3
-
151
-
-
0000675650
-
Modeling the bacterial photosynthetic reaction center. 1. Magnesium parameters for the semiempirical am1 method developed using a genetic algorithm
-
Hutter M, Reimers J, Hush N (1998) Modeling the bacterial photosynthetic reaction center. 1. Magnesium parameters for the semiempirical AM1 method developed using a genetic algorithm. J Phys Chem B 102:8080-8090
-
(1998)
J Phys Chem B
, vol.102
, pp. 8080-8090
-
-
Hutter, M.1
Reimers, J.2
Hush, N.3
-
152
-
-
0000295114
-
Modeling the bacterial photosynthetic reaction center. 2. A combined quantum mechanical molecular mechanical study of the structure of the cofactors in the reaction centers of purple bacteria
-
Hutter M, Hughes J, Reimers J, Hush N (1999) Modeling the bacterial photosynthetic reaction center. 2. A combined quantum mechanical molecular mechanical study of the structure of the cofactors in the reaction centers of purple bacteria. J Phys Chem B 103:4906-4915
-
(1999)
J Phys Chem B
, vol.103
, pp. 4906-4915
-
-
Hutter, M.1
Hughes, J.2
Reimers, J.3
Hush, N.4
-
153
-
-
0034719119
-
Modeling the bacterial photosynthetic reaction center 3: Interpretation of effects of site-directed mutagenesis on the special-pair midpoint potential
-
Reimers J, Hughes J, Hush N (2000) Modeling the bacterial photosynthetic reaction center 3: interpretation of effects of site-directed mutagenesis on the special-pair midpoint potential. Biochemistry 39:16185-16189
-
(2000)
Biochemistry
, vol.39
, pp. 16185-16189
-
-
Reimers, J.1
Hughes, J.2
Hush, N.3
-
154
-
-
0035812387
-
Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of rhodobacter sphaeroides
-
Hughes J, Hutter M, Reimers J, Hush N (2001) Modeling the bacterial photosynthetic reaction center. 4. The structural, electrochemical, and hydrogen-bonding properties of 22 mutants of Rhodobacter sphaeroides. J Am Chem Soc 123:8550-8563
-
(2001)
J Am Chem Soc
, vol.123
, pp. 8550-8563
-
-
Hughes, J.1
Hutter, M.2
Reimers, J.3
Hush, N.4
-
155
-
-
0042881116
-
Modelling the bacterial photosynthetic reaction center. V. Assignment of the electronic transition observed at 2200 cm(-1) in the specialpair radical-cation as a second-highest occupied molecular orbital to highest occupied molecular orbital transition
-
Reimers J, Shapley W, Hush N (2003) Modelling the bacterial photosynthetic reaction center. V. Assignment of the electronic transition observed at 2200 cm(-1) in the specialpair radical-cation as a second-highest occupied molecular orbital to highest occupied molecular orbital transition. J Chem Phys 119:3240-3248
-
(2003)
J Chem Phys
, vol.119
, pp. 3240-3248
-
-
Reimers, J.1
Shapley, W.2
Hush, N.3
-
156
-
-
0041878864
-
Modelling the bacterial photosynthetic reaction center. Vi. Use of densityfunctional theory to determine the nature of the vibronic coupling between the four lowest-energy electronic states of the specialpair radical cation
-
Reimers J, Shapley W, Rendell A, Hush N (2003) Modelling the bacterial photosynthetic reaction center. VI. Use of densityfunctional theory to determine the nature of the vibronic coupling between the four lowest-energy electronic states of the specialpair radical cation. J Chem Phys 119:3249-3261
-
(2003)
J Chem Phys
, vol.119
, pp. 3249-3261
-
-
Reimers, J.1
Shapley, W.2
Rendell, A.3
Hush, N.4
-
157
-
-
0041878862
-
Modeling the bacterial photosynthetic reaction center. Vii. Full simulation of the intervalence hole-transfer absorption spectrum of the special-pair radical cation
-
Reimers J, Hush N (2003) Modeling the bacterial photosynthetic reaction center. VII. Full simulation of the intervalence hole-transfer absorption spectrum of the special-pair radical cation. J Chem Phys 119:3262-3277
-
(2003)
J Chem Phys
, vol.119
, pp. 3262-3277
-
-
Reimers, J.1
Hush, N.2
-
158
-
-
56349143944
-
Theoretical investigation of the electronic asymmetry of the special pair cation radical in the photosynthetic type-ii reaction center
-
Yamasaki H, Takano Y, Nakamura H (2008) Theoretical investigation of the electronic asymmetry of the special pair cation radical in the photosynthetic type-II reaction center. J Phys Chem B 112:13923-13933
-
(2008)
J Phys Chem B
, vol.112
, pp. 13923-13933
-
-
Yamasaki, H.1
Takano, Y.2
Nakamura, H.3
-
159
-
-
33845341078
-
Protein-cofactor interactions in bacterial reaction centers from rhodobacter sphaeroides r-26: Effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study
-
Sinnecker S, Flores M, Lubitz W (2006) Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study. Phys Chem Chem Phys 8:5659-5670
-
(2006)
Phys Chem Chem Phys
, vol.8
, pp. 5659-5670
-
-
Sinnecker, S.1
Flores, M.2
Lubitz, W.3
-
160
-
-
0037426786
-
Structures and vibrational frequencies of the quinones in rb. Sphaeroides derived by a combined density functional/molecular mechanics approach
-
Nonella M, Mathias G, Eichinger M, Tavan P (2003) Structures and vibrational frequencies of the quinones in Rb. sphaeroides derived by a combined density functional/molecular mechanics approach. J Phys Chem B 107:316-322
-
(2003)
J Phys Chem B
, vol.107
, pp. 316-322
-
-
Nonella, M.1
Mathias, G.2
Eichinger, M.3
Tavan, P.4
-
161
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J (2000) Drug discovery: a historical perspective. Science 287:1960-1964
-
(2000)
Science
, vol.287
, pp. 1960-1964
-
-
Drews, J.1
-
162
-
-
77950650980
-
Towards accurate free energy calculations in ligand protein-binding studies
-
Steinbrecher T, Labahn A (2010) Towards accurate free energy calculations in ligand protein-binding studies. Curr Med Chem 17:767-785
-
(2010)
Curr Med Chem
, vol.17
, pp. 767-785
-
-
Steinbrecher, T.1
Labahn, A.2
-
163
-
-
33845873363
-
Development and validation of a modular, extensible docking program: Dock 5
-
Moustakas D, Lang P, Pegg S, Pettersen E, Kuntz I, Brooijmans N, Rizzo R (2006) Development and validation of a modular, extensible docking program: DOCK 5. J Comp Aided Mol Design 20:601-619
-
(2006)
J Comp Aided Mol Design
, vol.20
, pp. 601-619
-
-
Moustakas, D.1
Lang, P.2
Pegg, S.3
Pettersen, E.4
Kuntz, I.5
Brooijmans, N.6
Rizzo, R.7
-
164
-
-
6244283606
-
Critical evaluation of search algorithms for automated molecular docking and database screening
-
T.J.A. Ewing IK (1997) Critical evaluation of search algorithms for automated molecular docking and database screening. J Comp Chem 18:1175-1189
-
(1997)
J Comp Chem
, vol.18
, pp. 1175-1189
-
-
Ewing, T.J.A.I.K.1
-
165
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G, Goodsell D, Halliday R, Huey R, HartW, Belew R, Olson A (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 19:1639-1662
-
(1998)
J Comp Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.1
Goodsell, D.2
Halliday, R.3
Huey, R.4
Hart, W.5
Belew, R.6
Olson, A.7
-
166
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M, Kramer B, Lengauer T (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
167
-
-
0032738842
-
Evaluation of the flexx incremental construction algorithm for protein-ligand docking
-
Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Protein Struct Funct Genet 37:228-241
-
(1999)
Protein Struct Funct Genet
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
168
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen R, Leach A, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748
-
(1997)
J Mol Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.3
Leach, A.4
Taylor, R.5
-
169
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner R, Banks J, Murphy R, Halgren T, Klicic J, Mainz D, Repasky M, Knoll E, Shelley M, Perry J, Shaw D, Francis P, Shenkin P (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749
-
(2004)
J Med Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.1
Banks, J.2
Murphy, R.3
Halgren, T.4
Klicic, J.5
Mainz, D.6
Repasky, M.7
Knoll, E.8
Shelley, M.9
Perry, J.10
Shaw, D.11
Francis, P.12
Shenkin, P.13
-
170
-
-
1642310340
-
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
-
Halgren T, Murphy R, Friesner R, Beard H, Frye L, Pollard W, Banks J (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-1759
-
(2004)
J Med Chem
, vol.47
, pp. 1750-1759
-
-
Halgren, T.1
Murphy, R.2
Friesner, R.3
Beard, H.4
Frye, L.5
Pollard, W.6
Banks, J.7
-
171
-
-
24144448070
-
Are am1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
-
Villar R, Gil M, Garcia J, Martinez-Merino V (2005) Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? J Comp Chem 26:1347-1358
-
(2005)
J Comp Chem
, vol.26
, pp. 1347-1358
-
-
Villar, R.1
Gil, M.2
Garcia, J.3
Martinez-Merino, V.4
-
172
-
-
1542273631
-
Semiempirical calculations of binding enthalpy for protein-ligand complexes
-
Nikitina E, Sulimov V, Zayets V, Zaitseva N (2004) Semiempirical calculations of binding enthalpy for protein-ligand complexes. Int J Quant Chem 97:747-763
-
(2004)
Int J Quant Chem
, vol.97
, pp. 747-763
-
-
Nikitina, E.1
Sulimov, V.2
Zayets, V.3
Zaitseva, N.4
-
173
-
-
22244451417
-
Large-scale validation of a quantum mechanics based scoring function: Predicting the binding affinity and the binding mode of a diverse set of proteinligand complexes
-
Raha K, Merz K (2005) Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of proteinligand complexes. J Med Chem 48:4558-4575
-
(2005)
J Med Chem
, vol.48
, pp. 4558-4575
-
-
Raha, K.1
Merz, K.2
-
174
-
-
4944222323
-
Application of semiempirical quantum chemical methods as a scoring function in docking
-
Vasilyev V, Bliznyuk A (2004) Application of semiempirical quantum chemical methods as a scoring function in docking. Theo Chem Acc 112:313-317
-
(2004)
Theo Chem Acc
, vol.112
, pp. 313-317
-
-
Vasilyev, V.1
Bliznyuk, A.2
-
175
-
-
70350635655
-
A quantum mechanical approach to ligand binding -calculation of ligand-protein binding affinities for stromelysin-1 (mmp-3) inhibitors
-
Li J, Reynolds C (2009) A quantum mechanical approach to ligand binding -Calculation of ligand-protein binding affinities for stromelysin-1 (MMP-3) inhibitors. Can J Chem 87:1480-1484
-
(2009)
Can J Chem
, vol.87
, pp. 1480-1484
-
-
Li, J.1
Reynolds, C.2
-
176
-
-
33646875701
-
Quantum mechanics in structure-based drug design
-
Peters M, Raha K, Merz K (2006) Quantum mechanics in structure-based drug design. Curr Op Drug Disc 9:370-379
-
(2006)
Curr Op Drug Disc
, vol.9
, pp. 370-379
-
-
Peters, M.1
Raha, K.2
Merz, K.3
-
177
-
-
33846191945
-
Rank-ordering protein-ligand binding affinity by a quantum mechanics/molecular mechanics/poisson-boltzmann-surface area model
-
Wang M, Wong C (2007) Rank-ordering protein-ligand binding affinity by a quantum mechanics/molecular mechanics/Poisson-Boltzmann-surface area model. J Chem Phys 126:026101
-
(2007)
J Chem Phys
, vol.126
, pp. 026101
-
-
Wang, M.1
Wong, C.2
-
178
-
-
33747461412
-
Novel structural features of cdk inhibition revealed by an ab initio computational method combined with dynamic simulations
-
Heady L, Fernandez-Serra M, Mancera R, Joyce S, Venkitaraman A, Artacho E, Skylaris C, Ciacchi L, Payne M (2006) Novel structural features of CDK
-
(2006)
J Med Chem
, vol.49
, pp. 5141-5153
-
-
Heady, L.1
Fernandez-Serra, M.2
Mancera, R.3
Joyce, S.4
Venkitaraman, A.5
Artacho, E.6
Skylaris, C.7
Ciacchi, L.8
Payne, M.9
-
179
-
-
11144282711
-
Ab initio quantummechanical study of the binding energies of human estrogen receptor alpha with its ligands: An application of fragment molecular orbital method
-
Fukuzawa K, KitauraK,UebayasiM,NakataK, Kaminuma T, Nakano T (2005) Ab initio quantummechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method. J Comp Chem 26:1-10
-
(2005)
J Comp Chem
, vol.26
, pp. 1-10
-
-
Fukuzawa, K.1
Kitaura, K.2
Uebayasi, M.3
Nakata, K.4
Kaminuma, T.5
Nakano, T.6
-
180
-
-
39749175582
-
Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery
-
Fischer B, Fukuzawa K, Wenzel W (2008) Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery. Protein Struct Funct Genet 70:1264-1273
-
(2008)
Protein Struct Funct Genet
, vol.70
, pp. 1264-1273
-
-
Fischer, B.1
Fukuzawa, K.2
Wenzel, W.3
-
181
-
-
77449095294
-
Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies
-
Neugebauer J (2009) Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies. ChemPhysChem 10:3148-3173
-
(2009)
ChemPhysChem
, vol.10
, pp. 3148-3173
-
-
Neugebauer, J.1
-
182
-
-
77950225543
-
Computational photobiology and beyond
-
Schapiro I, Ryazantsev MN, Ding WJ, Huntress MM, Melaccio F, Andruniow T, Olivucci M (2010) Computational photobiology and beyond. Austr J Chem 63:413-429
-
(2010)
Austr J Chem
, vol.63
, pp. 413-429
-
-
Schapiro, I.1
Ryazantsev, M.N.2
Ding, W.J.3
Huntress, M.M.4
Melaccio, F.5
Andruniow, T.6
Olivucci, M.7
-
183
-
-
77951964891
-
Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes
-
Mata RA (2010) Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes. Phys Chem Chem Phys 12:5041-5052
-
(2010)
Phys Chem Chem Phys
, vol.12
, pp. 5041-5052
-
-
Mata, R.A.1
-
184
-
-
33747787695
-
Color tuning in rhodopsins: The mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin ii
-
Hoffmann M, Wanko M, Strodel P, Koenig PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, ElstnerM(2006) Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II. J Am Chem Soc 128:10808-10818
-
(2006)
J Am Chem Soc
, vol.128
, pp. 10808-10818
-
-
Hoffmann, M.1
Wanko, M.2
Strodel, P.3
Koenig, P.H.4
Frauenheim, T.5
Schulten, K.6
Thiel, W.7
Tajkhorshid, E.8
Elstner, M.9
-
185
-
-
67651207527
-
The infrared spectra of the retinal chromophore in bacteriorhodopsin calculated by a dft/mm approach
-
Babitzki G, Mathias G, Tavan P (2009) The infrared spectra of the retinal chromophore in bacteriorhodopsin calculated by a DFT/MM approach. J Phys Chem B 113:10496-10508
-
(2009)
J Phys Chem B
, vol.113
, pp. 10496-10508
-
-
Babitzki, G.1
Mathias, G.2
Tavan, P.3
-
186
-
-
34548730298
-
Quantum mechanics/molecular mechanics calculation of the raman spectra of the phycocyanobilin chromophore in alpha-cphycocyanin
-
Mroginski MA, Mark F, Thiel W, Hildebrandt P (2007) Quantum mechanics/molecular mechanics calculation of the Raman spectra of the phycocyanobilin chromophore in alpha-cphycocyanin. Biophys J 93:1885-1894
-
(2007)
Biophys J
, vol.93
, pp. 1885-1894
-
-
Mroginski, M.A.1
Mark, F.2
Thiel, W.3
Hildebrandt, P.4
-
187
-
-
68049137789
-
Chromophore structure of cyanobacterial phytochrome cph1 in the pr state: Reconciling structural and spectroscopic data by qm/mm calculations
-
Mroginski MA, von Stetten D, Escobar FV, Strauss HM, Kaminski S, Scheerer P, Guenther M, Murgida DH, Schmieder P, Bongards C, Gaertner W, Mailliet J, Hughes J, Essen LO, Hildebrandt P (2009) Chromophore structure of cyanobacterial phytochrome Cph1 in the Pr state: reconciling structural and spectroscopic data by QM/MM calculations. Biophys J 96:4153-4163
-
(2009)
Biophys J
, vol.96
, pp. 4153-4163
-
-
Mroginski, M.A.1
Von Stetten, D.2
Escobar, F.V.3
Strauss, H.M.4
Kaminski, S.5
Scheerer, P.6
Guenther, M.7
Murgida, D.H.8
Schmieder, P.9
Bongards, C.10
Gaertner, W.11
Mailliet, J.12
Hughes, J.13
Essen, L.O.14
Hildebrandt, P.15
-
188
-
-
77951201150
-
Raman spectra of the phycoviolobilin cofactor in phycoerythrocyanin calculated by qm/mm methods
-
Mroginski MA, Kaminski S, Hildebrandt P (2010) Raman spectra of the phycoviolobilin cofactor in phycoerythrocyanin calculated by QM/MM methods. ChemPhysChem 11:1265-1274
-
(2010)
ChemPhysChem
, vol.11
, pp. 1265-1274
-
-
Mroginski, M.A.1
Kaminski, S.2
Hildebrandt, P.3
-
189
-
-
22944450867
-
Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application
-
SchmitzM,Tavan P (2004) Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application. J Chem Phys 121:12233-12246
-
(2004)
J Chem Phys
, vol.121
, pp. 12233-12246
-
-
Schmitz, M.1
Tavan, P.2
-
190
-
-
22944442956
-
Vibrational spectra from atomic fluctuations in dynamics simulations. Ii. Solvent-induced frequency fluctuations at femtosecond time resolution
-
Schmitz M, Tavan P (2004) Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution. J Chem Phys 121:12247-12258
-
(2004)
J Chem Phys
, vol.121
, pp. 12247-12258
-
-
Schmitz, M.1
Tavan, P.2
-
191
-
-
77951143605
-
Vibrational raman spectra from the self-consistent charge density functional tight binding method via classical time-correlation functions
-
Kaminski S, Gaus M, Phatak P, von Stetten D, Elstner M, Mroginski MA (2010) Vibrational Raman spectra from the self-consistent charge density functional tight binding method via classical time-correlation functions. J Chem Theor Comput 6:1240-1255
-
(2010)
J Chem Theor Comput
, vol.6
, pp. 1240-1255
-
-
Kaminski, S.1
Gaus, M.2
Phatak, P.3
Von Stetten, D.4
Elstner, M.5
Mroginski, M.A.6
-
192
-
-
37549043500
-
The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding
-
Yu H, Cui Q (2007) The vibrational spectra of protonated water clusters: a benchmark for self-consistent-charge density-functional tight binding. J Chem Phys 127:234504
-
(2007)
J Chem Phys
, vol.127
, pp. 234504
-
-
Yu, H.1
Cui, Q.2
-
193
-
-
58149376459
-
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin
-
Phatak P, Ghosh N, Yu H, Cui Q, Elstner M (2008) Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci USA 105:19672-19677
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 19672-19677
-
-
Phatak, P.1
Ghosh, N.2
Yu, H.3
Cui, Q.4
Elstner, M.5
-
194
-
-
77955558974
-
Hydrogen bonds rebuilt by polarized protein-specific charges
-
Xu Z,Mei Y,Duan L,ZhangD(2010)Hydrogen bonds rebuilt by polarized protein-specific charges. Chem Phys Lett 495:151-154
-
(2010)
Chem Phys Lett
, vol.495
, pp. 151-154
-
-
Xu, Z.1
Mei, Y.2
Duan, L.3
Zhang, D.4
-
195
-
-
63149159310
-
Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization
-
Duan LL, Mei Y, Zhang QG, Zhang JZH (2009) Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization. J Chem Phys 130:115102
-
(2009)
J Chem Phys
, vol.130
, pp. 115102
-
-
Duan, L.L.1
Mei, Y.2
Zhang, Q.G.3
Zhang, J.Z.H.4
-
196
-
-
77956073656
-
The protonation state of glu181 in rhodopsin revisited: Interpretation of experimental data on the basis of qm/mm calculations
-
Fraehmcke JS, Wanko M, Phatak P, Mroginski MA, Elstner M (2010) The protonation state of glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B 114:11338-11352
-
(2010)
J Phys Chem B
, vol.114
, pp. 11338-11352
-
-
Fraehmcke, J.S.1
Wanko, M.2
Phatak, P.3
Mroginski, M.A.4
Elstner, M.5
-
197
-
-
14844348202
-
Calculating absorption shifts for retinal proteins: Computational challenges
-
Wanko M, Hoffmann M, Strodel P, Koslowski A, Thiel W, Neese F, Frauenheim T, Elstner M (2005) Calculating absorption shifts for retinal proteins: Computational challenges. J Phys Chem B 109:3606-3615
-
(2005)
J Phys Chem B
, vol.109
, pp. 3606-3615
-
-
Wanko, M.1
Hoffmann, M.2
Strodel, P.3
Koslowski, A.4
Thiel, W.5
Neese, F.6
Frauenheim, T.7
Elstner, M.8
-
198
-
-
28544448728
-
Singlereference ab initio methods for the calculation of excited states of large molecules
-
Dreuw A, Head-Gordon M (2005) Singlereference ab initio methods for the calculation of excited states of large molecules. Chem Rev 105:4009-4037
-
(2005)
Chem Rev
, vol.105
, pp. 4009-4037
-
-
Dreuw, A.1
Head-Gordon, M.2
-
199
-
-
33751325382
-
Quantum chemical methods for the investigation of photoinitiated processes in biological systems: Theory and applications
-
Dreuw A (2006) Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications. ChemPhysChem 7:2259-2274
-
(2006)
ChemPhysChem
, vol.7
, pp. 2259-2274
-
-
Dreuw, A.1
-
200
-
-
1242264766
-
A global investigation of excited state surfaces within time-dependent density-functional response theory
-
Wanko M, Garavelli M, Bernardi F, Niehaus T, Frauenheim T, Elstner M (2004) A global investigation of excited state surfaces within time-dependent density-functional response theory. J Chem Phys 120:1674-1692
-
(2004)
J Chem Phys
, vol.120
, pp. 1674-1692
-
-
Wanko, M.1
Garavelli, M.2
Bernardi, F.3
Niehaus, T.4
Frauenheim, T.5
Elstner, M.6
-
201
-
-
53049106598
-
Effect of polarization on the opsin shift in rhodopsins. 1. A combined qm/qm/mm model for bacteriorhodopsin and pharaonis sensory rhodopsin ii
-
Wanko M, Hoffmann M, Frauenheim T, Elstner M (2008) Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II. J Phys Chem B 112:11462-11467
-
(2008)
J Phys Chem B
, vol.112
, pp. 11462-11467
-
-
Wanko, M.1
Hoffmann, M.2
Frauenheim, T.3
Elstner, M.4
-
202
-
-
53049096961
-
Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins
-
Wanko M, Hoffmann M, Fraehmcke J, Frauenheim T, Elstner M (2008) Effect of polarization on the opsin shift in rhodopsins. 2. Empirical polarization models for proteins. J Phys Chem B 112:11468-11478
-
(2008)
J Phys Chem B
, vol.112
, pp. 11468-11478
-
-
Wanko, M.1
Hoffmann, M.2
Fraehmcke, J.3
Frauenheim, T.4
Elstner, M.5
-
203
-
-
65349179259
-
Protein influence on electronic spectra modeled by multipoles and polarizabilities
-
Soederhjelm P, Husberg C, Strambi A, Olivucci M, Ryde U (2009) Protein influence on electronic spectra modeled by multipoles and polarizabilities. J Chem Theor Comput 5:649-658
-
(2009)
J Chem Theor Comput
, vol.5
, pp. 649-658
-
-
Soederhjelm, P.1
Husberg, C.2
Strambi, A.3
Olivucci, M.4
Ryde, U.5
-
204
-
-
84892860354
-
-
Ph.D. thesis, Technical University of Braunschweig, Germany
-
Wanko M (2008) Ph.D. thesis, Technical University of Braunschweig, Germany
-
(2008)
-
-
Wanko, M.1
-
205
-
-
70349112722
-
Long-distance proton transfer with a break in the bacteriorhodopsin active site
-
Phatak P, Fraehmcke JS, Wanko M, Hoffmann M, Strodel P, Smith JC, Suhai S, Bondar AN, Elstner M (2009) Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc 131:7064-7078
-
(2009)
J Am Chem Soc
, vol.131
, pp. 7064-7078
-
-
Phatak, P.1
Fraehmcke, J.S.2
Wanko, M.3
Hoffmann, M.4
Strodel, P.5
Smith, J.C.6
Suhai, S.7
Bondar, A.N.8
Elstner, M.9
-
206
-
-
36649021120
-
Design of a next generation force field: The x-pol potential
-
Xie W, Gao J (2007) Design of a next generation force field: the X-POL potential. J Chem Theor Comput 3:1890-1900
-
(2007)
J Chem Theor Comput
, vol.3
, pp. 1890-1900
-
-
Xie, W.1
Gao, J.2
-
207
-
-
36649010414
-
Anisotropic, polarizable molecular mechanics studies of inter-And intramoecular interactions and ligand-macromolecule complexes. A bottom-up strategy
-
Gresh N, Cisneros GA, Darden TA, Piquemal JP (2007) Anisotropic, polarizable molecular mechanics studies of inter-And intramoecular interactions and ligand-macromolecule complexes. A bottom-up strategy. J Chem Theor Comput 3:1960-1986
-
(2007)
J Chem Theor Comput
, vol.3
, pp. 1960-1986
-
-
Gresh, N.1
Cisneros, G.A.2
Darden, T.A.3
Piquemal, J.P.4
|