-
1
-
-
0032079636
-
Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics
-
Shirai, H., Nakajima, N., Higo, J., Kidera, A. and Nakamura, H.: Conformational sampling of CDR-H3 in antibodies by multicanonical molecular dynamics, J. Mol. Biol. 278 (1998), 481-496.
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 481-496
-
-
Shirai, H.1
Nakajima, N.2
Higo, J.3
Kidera, A.4
Nakamura, H.5
-
2
-
-
0344642583
-
Enhanced conformational diversity search of CDR-H3 in antibodies: Role of the first CDR-H3 residue
-
Kim, S.T., Shirai, N., Nakajima, N. and Nakamura, H.: Enhanced conformational diversity search of CDR-H3 in antibodies: Role of the first CDR-H3 residue, Proteins: Struct. Funct. Genet. 37 (1999), 683-696.
-
(1999)
Proteins: Struct. Funct. Genet.
, vol.37
, pp. 683-696
-
-
Kim, S.T.1
Shirai, N.2
Nakajima, N.3
Nakamura, H.4
-
3
-
-
0031592919
-
Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
-
Nakajima, N., Higo, J., Kidera, A. and Nakamura, H.: Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation, Chem. Phys. Lett. 278 (1997), 297-301.
-
(1997)
Chem. Phys. Lett.
, vol.278
, pp. 297-301
-
-
Nakajima, N.1
Higo, J.2
Kidera, A.3
Nakamura, H.4
-
4
-
-
0034635351
-
Free energy landscapes of peptides by enhanced conformational sampling
-
Nakajima, N., Higo, J., Kidera, A. and Nakamura, H.: Free energy landscapes of peptides by enhanced conformational sampling, J. Mol. Biol. 296 (2000), 197-216.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 197-216
-
-
Nakajima, N.1
Higo, J.2
Kidera, A.3
Nakamura, H.4
-
5
-
-
0001095973
-
Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics
-
Higo, J., Galzitskaya, O.V., Ono, S. and Nakamura, H.: Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics, Chem. Phys. Lett. 337 (2001), 169-175.
-
(2001)
Chem. Phys. Lett.
, vol.337
, pp. 169-175
-
-
Higo, J.1
Galzitskaya, O.V.2
Ono, S.3
Nakamura, H.4
-
6
-
-
0035008585
-
10-Helix, β-Turn, β-Hairpin and other disordered conformations
-
10-Helix, β-Turn, β-Hairpin and other disordered conformations, Protein Sci. 10 (2001), 1160-1171.
-
(2001)
Protein Sci.
, vol.10
, pp. 1160-1171
-
-
Higo, J.1
Ito, N.2
Kuroda, M.3
Ono, S.4
Nakajima, N.5
Nakamura, H.6
-
7
-
-
0000626498
-
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
-
Ono, S., Nakajima, N., Higo, J. and Nakamura, H.: Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95, J. Comput. Chem. 21 (2000), 748-762.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 748-762
-
-
Ono, S.1
Nakajima, N.2
Higo, J.3
Nakamura, H.4
-
8
-
-
0031232794
-
Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo. Water clusters and bulk water
-
Samuelson, S., Tobias, D.J., Martyna, G.J.: Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo. Water clusters and bulk water, J. Phys. Chem. 101B (1997), 7592-7603.
-
(1997)
J. Phys. Chem.
, vol.101 B
, pp. 7592-7603
-
-
Samuelson, S.1
Tobias, D.J.2
Martyna, G.J.3
-
9
-
-
0029011701
-
A second generation force field for the simulation of proteins. Nucleic acids and organic molecules
-
Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K.M., Jr., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.: A second generation force field for the simulation of proteins. Nucleic Acids and Organic Molecules, J. Am. Chem. Soc. 117 (1995), 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz K.M., Jr.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.10
-
10
-
-
0002098417
-
The development/application of a 'Minimalist' organic/biochemical molecular mechanics force field using a combination of ab initio calculations and experimental data
-
W.F. van Gunsteren, P.K. Weiner and A.J. Wilkinson (eds.). Kluwer/ESCOM, The Netherlands
-
Kollman, P., Dixon, R., Cornell, W., Fox, T., Chipot, C. and Pohorille, A.: The development/application of a 'Minimalist' organic/biochemical molecular mechanics force field using a combination of ab initio calculations and experimental data, In: W.F. van Gunsteren, P.K. Weiner and A.J. Wilkinson (eds.), Computer Simulation of Biomolecular Systems 3, Kluwer/ESCOM, The Netherlands, 1997, pp. 83-96.
-
(1997)
Computer Simulation of Biomolecular Systems 3
, pp. 83-96
-
-
Kollman, P.1
Dixon, R.2
Cornell, W.3
Fox, T.4
Chipot, C.5
Pohorille, A.6
-
11
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, Jr., A.D., Bashford, D., Bellott, M., Dunbrack, Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kichnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, III, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M.: All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. 102B (1998), 3586-3616.
-
(1998)
J. Phys. Chem.
, vol.102 B
, pp. 3586-3616
-
-
MacKerell A.D., Jr.1
Bashford, D.2
Bellott, M.3
Dunbrack R.L., Jr.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kichnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher W.E. III20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
12
-
-
0036489113
-
Calibration of force field dependency in free energy landscapes of peptide conformations by quantum chemical calculations
-
in press
-
Ono, S., Kuroda, M., Higo, J., Nakajima, N. and Nakamura, H.: Calibration of force field dependency in free energy landscapes of peptide conformations by quantum chemical calculations, J. Comput. Chem., in press.
-
J. Comput. Chem.
-
-
Ono, S.1
Kuroda, M.2
Higo, J.3
Nakajima, N.4
Nakamura, H.5
-
13
-
-
22844453568
-
A general ab initio approach for free energy landscapes of biological molecules around the transition states
-
Nakamura, H., Ono, S. and Higo, J.: A general ab initio approach for free energy landscapes of biological molecules around the transition states. Proc. Japan Acad. 75B (1999), 291-294.
-
(1999)
Proc. Japan Acad.
, vol.75 B
, pp. 291-294
-
-
Nakamura, H.1
Ono, S.2
Higo, J.3
-
14
-
-
0008348735
-
Vectorized molecular mechanics program for biopolymers
-
Morikami, K., Nakai, T., Kidera, A., Saito, M. and Nakamura, H.: PRESTO: A vectorized molecular mechanics program for biopolymers, Comput. Chem. 16 (1992), 243-248.
-
(1992)
Comput. Chem.
, vol.16
, pp. 243-248
-
-
Morikami, K.1
Nakai, T.2
Kidera, A.3
Saito, M.4
Nakamura, H.5
Presto, A.6
-
15
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid qater
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L.: Comparison of simple potential functions for simulating liquid qater. J. Chem. Phys. 79 (1983), 926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
16
-
-
0000617302
-
High-strain-rate plastic flow studied via nonequilibrium molecular dynamics
-
Hoover, W.G., Ladd, A.J.C. and Moran, B.: High-strain-rate plastic flow studied via nonequilibrium molecular dynamics, Phys. Rev. Lett. 48 (1982), 1818-1820.
-
(1982)
Phys. Rev. Lett.
, vol.48
, pp. 1818-1820
-
-
Hoover, W.G.1
Ladd, A.J.C.2
Moran, B.3
-
17
-
-
5244222040
-
The isothermal/isobaric molecular dynamics ensemble
-
Evans, D.J. and Morris, G.P.: The isothermal/isobaric molecular dynamics ensemble, Phys. Lett. 98A (1983), 433-436.
-
(1983)
Phys. Lett.
, vol.98 A
, pp. 433-436
-
-
Evans, D.J.1
Morris, G.P.2
-
18
-
-
33646940952
-
Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-Alkanes
-
Ryckaert, J.-P., Ciccotti, G. and Berendsen, H.J.C.: Numerical integration of cartesian equations of motion of a system with constraints: Molecular dynamics of n-Alkanes, J. Comput. Phys. 23 (1977), 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.-P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
19
-
-
0004133516
-
-
Gaussian, Inc., Pittsburgh PA
-
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Zakzewski, V.G., Montgomery, J.A., Stratmann, R.E., J.C.Burant, J.C., Dapprich, S., Millam, J.M., Daniels, A.D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Adamo, C.P.C., Clifford, S., Ochterski, J., Petersson, G.A., Ayala, P.Y., Cui, Q., Morokuma, K., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., Ortiz, J.V., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P.M.W., Johnson, B.G., Chen, W., Wong, M.W., Andres, J.L., Head-Gordon, M., Replogle, E.S. and Pople, J.A.: Gaussian 98 (Revision A6), Gaussian, Inc., Pittsburgh PA, 1998.
-
(1998)
Gaussian 98 (Revision A6)
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Zakzewski, V.G.7
Montgomery, J.A.8
Stratmann, R.E.9
Burant, J.C.10
Dapprich, S.11
Millam, J.M.12
Daniels, A.D.13
Kudin, K.N.14
Strain, M.C.15
Farkas, O.16
Tomasi, J.17
Barone, V.18
Cossi, M.19
Cammi, R.20
Mennucci, B.21
Adamo, C.P.C.22
Clifford, S.23
Ochterski, J.24
Petersson, G.A.25
Ayala, P.Y.26
Cui, Q.27
Morokuma, K.28
Malick, D.K.29
Rabuck, A.D.30
Raghavachari, K.31
Foresman, J.B.32
Cioslowski, J.33
Ortiz, J.V.34
Stefanov, B.B.35
Liu, G.36
Liashenko, A.37
Piskorz, P.38
Komaromi, I.39
Gomperts, R.40
Martin, R.L.41
Fox, D.J.42
Keith, T.43
Al-Laham, M.A.44
Peng, C.Y.45
Nanayakkara, A.46
Gonzalez, C.47
Challacombe, M.48
Gill, P.M.W.49
Johnson, B.G.50
Chen, W.51
Wong, M.W.52
Andres, J.L.53
Head-Gordon, M.54
Replogle, E.S.55
Pople, J.A.56
more..
-
20
-
-
0025679019
-
Reverse turns in blocked dipeptides are intrinsically unstable in water
-
Tobias, D.J., Sneddon, S.F. and Brooks, C.L., III: Reverse turns in blocked dipeptides are intrinsically unstable in water, J. Mol. Biol. 216 (1990), 783-796.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 783-796
-
-
Tobias, D.J.1
Sneddon, S.F.2
Brooks C.L. III3
-
21
-
-
0030745939
-
Accurate ab initio quantum chemical determination of the relative energies of peptide conformations and assessment of empirical force fields
-
Beachy, M.D., Chasman, D., Murphy, R.B., Halgren, T.A. and Friesner, R.A.: Accurate ab initio quantum chemical determination of the relative energies of peptide conformations and assessment of empirical force fields, J. Am. Chem. Soc. 119 (1997), 5908-5920.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 5908-5920
-
-
Beachy, M.D.1
Chasman, D.2
Murphy, R.B.3
Halgren, T.A.4
Friesner, R.A.5
-
22
-
-
0035913529
-
Evaluation of reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminsky, G.A., Friesner, R.A., Tirado-Rives, J. and Jorgensen, W.L.: Evaluation of reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides, J. Phys. Chem. 105B (2001), 6474-6487.
-
(2001)
J. Phys. Chem.
, vol.105 B
, pp. 6474-6487
-
-
Kaminsky, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
23
-
-
0000025377
-
The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths
-
Ono, S., Nakajima, N., Higo, J. and Nakamura, H.: The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths, Chem. Phys. Lett. 312 (1999), 247-254.
-
(1999)
Chem. Phys. Lett.
, vol.312
, pp. 247-254
-
-
Ono, S.1
Nakajima, N.2
Higo, J.3
Nakamura, H.4
|