- Prediction of three-dimensional structures of biomolecules such as
proteins by computer simulations

- Development of effective generalized-ensemble algorithms for molecular simulations

- Y. Okamoto, "Protein folding problem as studied by new simulation algorithms,"
*Recent Research Developments in Pure & Applied Chemistry***2**, 1 - 23 (1998).

- U.H.E. Hansmann and Y. Okamoto,
"The generalized-ensemble approach for protein folding simulations,"
in
*Annual Reviews of Computational Physics VI*, D. Stauffer (ed.) (World Scientific, Singapore, 1999), pp. 129-157.

- U.H.E. Hansmann and Y. Okamoto,
"New Monte Carlo algorithms for protein folding,"
*Current Opinion in Structural Biology***9**, 177 - 183 (1999).

- Y. Okamoto and U.H.E. Hansmann,
"Protein folding simulations by a generalized-ensemble algorithm based on Tsallis statistics,"
in
*Lecture Notes in Physics: Nonextensive Statistical Mechanics and Its Applications*, S. Abe and Y. Okamoto (eds.) (Springer-Verlag, Berlin, 2001), pp. 259 - 274.

- A. Mitsutake, Y. Sugita, and Y. Okamoto, "Generalized-ensemble algorithms for molecular simulations of biopolymers," (PDF: 984 KB)
*Biopolymers (Peptide Science)***60**, 96 - 123 (2001).

- Y. Sugita and Y. Okamoto,
"Free-energy
calculations in protein folding by
generalized-ensemble algorithms," (PDF: 492 KB)
in
*Lecture Notes in Computational Science and Engineering*, T. Schlick and H.H. Gan (eds.) (Springer-Verlag, Berlin, 2002), pp. 303 - 331.

- Y. Okamoto, "Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and
molecular dynamics simulations,"
*Journal of Molecular Graphics and Modelling***22**, 425 - 439 (2004).

- H. Kawai, T. Kikuchi, and Y. Okamoto,
"A prediction of tertiary structures of peptide by the
Monte Carlo simulated annealing method,"
*Protein Engineering***3**, 85 - 94 (1989).

- Y. Okamoto, M. Fukugita, T. Nakazawa, and H. Kawai,
"ƒ¿-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of
ribonuclease A,"
*Protein Engineering***4**, 639 - 647 (1991).

- T. Nakazawa, H. Kawai, Y. Okamoto, and M. Fukugita,
"ƒÀ-Sheet folding of bovine pancreatic trypsin inhibitor fragment [16-36] as
predicted by Monte Carlo simulated annealing,"
*Protein Engineering***5**, 495 - 503 (1992).

- U.H.E. Hansmann and Y. Okamoto,
"Prediction of peptide conformation by multicanonical
algorithm: new approach to the multiple-minima problem,"
*Journal of Computational Chemistry***14**, 1333 - 1338 (1993).

- Y. Okamoto and U.H.E. Hansmann,
"Thermodynamics of helix-coil transitions studied by multicanonical algorithms,"
*Journal of Physical Chemistry***99**, 11276 - 11287 (1995).

- U.H.E. Hansmann, Y. Okamoto, and F. Eisenmenger,
"Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble,"
*Chemical Physics Letters***259**, 321 - 330 (1996).

- U.H.E. Hansmann and Y. Okamoto,
"Numerical comparisons of three recently proposed algorithms in the
protein folding problem,"
*Journal of Computational Chemistry***18**, 920 - 933 (1997).

- U.H.E. Hansmann and Y. Okamoto,
"Generalized-ensemble Monte Carlo method for systems with rough energy
landscape,"
*Physical Review E***56**, 2228 - 2233 (1997).

- U.H.E. Hansmann, M. Masuya, and Y. Okamoto,
"Characteristic temperatures of folding of a small peptide,"
*Proceedings of National Academy of Sciences USA***94**, 10652 - 10656 (1997).

- M. Kinoshita, Y. Okamoto, and F. Hirata,
"Calculation of hydration free energy for a solute with many atomic sites
using the RISM theory: robust and efficient algorithm,"
*Journal of Computational Chemistry***18**, 1320 - 1326 (1997).

- U.H.E. Hansmann, Y. Okamoto, and J.N. Onuchic,
"The folding funnel landscape for the peptide Met-enkephalin,"
*PROTEINS: Structure, Function, and Genetics***34**, 472 - 483 (1999).

- A. Mitsutake, M. Irisa, Y. Okamoto, and F. Hirata,
"Classification of low-energy conformations of Met-enkephalin in the gas phase
and in a model solvent based on the extended scaled particle theory,"
*Bulletin of the Chemical Society of Japan***72**, 1717 - 1729 (1999).

- Y. Sugita and Y. Okamoto,
"Replica-exchange molecular dynamics method for protein folding,"
*Chemical Physics Letters***314**, 141 - 151 (1999).

- A. Mitsutake and Y. Okamoto,
"Helix-coil transitions of amino-acid homo-oligomers in aqueous solution studied by
multicanonical simulations,"
*Journal of Chemical Physics***112**, 10638 - 10647 (2000).

- Y. Sugita and Y. Okamoto,
"Replica-exchange multicanonical algorithm and multicanonical
replica-exchange method for simulating systems with rough energy landscape,"
*Chemical Physics Letters***329**, 261 - 270 (2000).

- A. Mitsutake and Y. Okamoto,
"Replica-exchange simulated tempering method for simulations of frustrated systems,"
*Chemical Physics Letters***332**, 131 - 138 (2000).

- Y. Sugita, A. Kitao, and Y. Okamoto,
"Multidimensional replica-exchange method for free-energy calculations,"
*Journal of Chemical Physics***113**, 6042 - 6051 (2000).

- M. Kinoshita, Y. Okamoto, and F. Hirata,
"Peptide conformations in alcohol and water: analyses by the reference interaction
site model theory,"
*Journal of the American Chemical Society***122**, 2773 - 2779 (2000).

- T. Nishikawa, H. Ohtsuka, Y. Sugita, M. Mikami, and Y. Okamoto,
"Replica-exchange Monte Carlo method for Ar fluid,"
*Progress of Theoretical Physics Supplement*No.**138**, 270 - 271 (2000).

- Y. Ishikawa, Y. Sugita, T. Nishikawa, and Y. Okamoto,
"Ab initio replica-exchange Monte Carlo method for cluster studies,"
*Chemical Physics Letters***333**, 199 - 206 (2001).

- T. Nagasima, Y. Sugita, A. Mitsutake, and Y. Okamoto,
"Generalized-ensemble simulations of spin systems and protein systems,"
*Computer Physics Communications***146**, 69 - 76 (2002).

- T. Hiroyasu, M. Miki, M. Ogura, and Y. Okamoto,
"Examination of parallel simulated annealing using genetic crossover," (in Japanese),
*IPSJ TOM***43**, 70 - 79 (2002). - A. Mitsutake, Y. Sugita, and Y. Okamoto,
"Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo
simulations of peptides,"
*Journal of Chemical Physics***118**, 6664 - 6675 (2003);*ibid.***118**, 6676 - 6688 (2003).

- G. La Penna, A. Mitsutake, M. Masuya, and Y. Okamoto,
"Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange
Monte Carlo method and diffusion theory,"
*Chemical Physics Letters***380**, 609 - 619 (2003).

- B.A. Berg, H. Noguchi, and Y. Okamoto,
"Multioverlap simulations for transitions between reference configurations,"
*Physical Review E***68**, 036126 (11 pages) (2003).

- Y. Sakae and Y. Okamoto,
"Optimization of protein force-field parameters with the Protein Data Bank,"
*Chemical Physics Letters***382**, 626 - 636 (2003).

- H. Okumura and Y. Okamoto,
"Monte Carlo simulations in multibaric-multithermal ensemble,"
*Chemical Physics Letters***383**, 391 - 396 (2004).

- H. Kokubo and Y. Okamoto,
"Prediction of transmembrane helix configurations by replica-exchange simulations,"
*Chemical Physics Letters***383**, 397 - 402 (2004).

- K. Murata, Y. Sugita, and Y. Okamoto,
"Free energy calculations for DNA base stacking by replica-exchange umbrella sampling,"
*Chemical Physics Letters***385**, 1 - 7 (2004).

- T. Yoda, Y. Sugita, and Y. Okamoto,
"Comparisons of force fields for proteins by generalized-ensemble simulations,"
*Chemical Physics Letters***386**, 460 - 467 (2004).

- C. Muguruma, Y. Okamoto, and M. Mikami,
"New approach to the first-order phase transition of Lennard-Jones fluids,"
*Journal of Chemical Physics***120**, 7557 - 7563 (2004).

- H. Okumura and Y. Okamoto,
"Molecular dynamics simulations in the multibaric-multithermal ensemble,"
*Chemical Physics Letters***391**, 248 - 253 (2004).

- H. Kokubo and Y. Okamoto,
"Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange
Monte Carlo simulation,"
*Chemical Physics Letters***392**, 168 - 175 (2004).

- A. Mitsutake and Y. Okamoto,
"Replica-exchange extensions of simulated tempering method,"
*Journal of Chemical Physics***121**, 2491 - 2504 (2004).

- H. Okumura and Y. Okamoto,
"Monte Carlo simulations in generalized isobaric-isothermal ensembles,"
*Physical Review E***70**, 026702 (14 pages) (2004).

- H. Kokubo and Y. Okamoto,
"Classification and prediction of low-energy membrane protein helix configurations by
replica-exchange Monte Carlo method,"
*Journal of the Physical Society of Japan***73**, 2571 - 2585 (2004).

- H. Okumura and Y. Okamoto,
"Liquid-gas phase transition studied by multibaric-multithermal Monte Carlo
simulations,"
*Journal of the Physical Society of Japan***73**, 3304 - 3311 (2004).

- A. Mitsutake, M. Kinoshita, Y. Okamoto, and F. Hirata,
"Combination of the replica-exchange Monte Carlo method and the reference interaction
site model theory for simulating a peptide molecule in aqueous solution,"
*Journal of Physical Chemistry B***108**, 19002 - 19012 (2004).

- S.G.. Itoh and Y. Okamoto,
"Multi-overlap molecular dynamics methods for biomolecular systems,"
*Chemical Physics Letters***400**, 308 - 313 (2004).

- Y. Sugita and Y. Okamoto,
"Molecular mechanism for stabilizing a short helical peptide studied by
generalized-ensemble simulations with explicit solvent,"
*Biophysical Journal***88**, 3180 - 3190 (2005).

- K. Yoshida, T. Yamaguchi, and Y. Okamoto,
"Replica-exchange molecular dynamics simulation of small peptide in water and in
ethanol,"
*Chemical Physics Letters***412**, 280 - 284 (2005).

- M. Nishino, Y. Sugita, T. Yoda, and Y. Okamoto,
"Structures of a peptide fragment of beta2-microglobulin studied by replica-exchange
molecular dynamics simulations - towards the understanding of the mechanism of
amyloid formation,"
*FEBS Letters***579**, 5425 - 5429 (2005).

- K. Kawashima, Y. Sugita, T. Yoda, and Y. Okamoto,
"Effects of the fixed end in single-molecule imaging techniques: A replica-exchange
molecular dynamics study,"
*Chemical Physics Letters***414**, 449 - 455 (2005).

- H. Okumura and Y. Okamoto,
"Multibaric-multithermal ensemble molecular dynamics simulations,"
*Journal of Computational Chemistry***27**, 379 - 395 (2006).

- S.G. Itoh and Y. Okamoto,
"Theoretical studies of transition states by the multi-overlap molecular dynamics methods,"
*Journal of Chemical Physics***124**, 104103 (14 pages) (2006).

- Y. Sakae and Y. Okamoto,
"Secondary-structure design of proteins by a backbone torsion energy,"
*Journal of the Physical Society of Japan***75**, 054802 (9 pages) (2006).

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