Publications
Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis.
Wako, H. and Endo, S.
Biophys. Chem. (2011) 159:257-266. [doi:10.1016/j.bpc.2011.07.004]
Folding/unfolding kinetics of lattice proteins
by applying a simple statistical mechanical model for protein folding.
Wako, H. and Abe, H.
In Protein Folding, E.C. Walters Ed., Nova Science Publishers, Inc., N.Y. (2011) 349-376.
PDF is downloadable freely at NOVA publishers
Prediction of protein motions from amino
acid sequence and its application to protein-protein interaction.
Hirose,S., Yokota, K., Kuroda, Y., Wako, H., Endo, S.,
Kanai, S., and Noguchi, T.
BMC Structural Biology (2010) 10:20. [doi:10.1186/1472-6807-10-20]
Folding/unfolding kinetics of lattice
proteins studied using a simple statistical mechanical model for protein
folding, I: Dependence on native structures and amino acid sequences.
Abe, H. and Wako, H.
Physica A (2009) 388,
3442-3454. [doi:
10.1016/j.physa.2009.05.020]
Single Amino
Acid Substitutions in Lattice Proteins Using Statistical Mechanical Model for
Protein Folding.
Wako, H. and Abe, H.
J. Phys. Soc. Jpn (2007) 76,
104801. [doi:
10.1143/JPSJ.76.104801]
Statistical
Mechanical Theory of Protein Conformation and Its Transition.
Kobayashi, Y., Wako, H.
and Saito, N.
J. Phys. Soc. Jpn (2007) 76,
074802. [doi:
10.1143/JPSJ.76.074802]
Analyses of
simulations of three-dimensional lattice proteins in comparison with a
simplified statistical mechanical model of protein folding.
Abe, H. and Wako, H.
Phys. Rev. E (2006) 74, 011913. [doi:
10.1103/PhysRevE.74.011913]
ProMode: a
database of normal mode analyses on protein molecules with a full-atom model.
Wako, H., Kato, M. & Endo,
Bioinformatics
Database: ProMode is
available at http://promode.socs.waseda.ac.jp/.
Application of a
statistical mechanical model for protein folding to a three-dimensional lattice
protein.
Abe, H. & Wako, H.
J. Phys. Soc. Jpn (2004) 73,
1143-1146 [doi:
10.1143/JPSJ.73.1143]
Environment-dependent
and position-specific frequencies of amino acid occurrences in α-helices.
Wako, H., An, J. & Sarai, A.
Chem-Bio Info. J (2003) 3, 58-77 [abstract]
[Full-text.pdf]
Improvements in ProMode (a database of normal mode analyses of proteins).
Wako, H., Kato, M. & Endo, S.
Genome Informatics (2003) 14, 663-664 [Full-text.pdf]
ProMode: A
database of normal mode analysis of proteins.
Wako, H. & Endo, S.
Genome Informatics (2002) 13, 519-520 [Full-text.pdf]
Sampling efficiency of molecular
dynamics and
Yamashita, H., Endo, S., Wako, H. & Kidera, A.
Chem. Phys. Lett. (2001) 342, 382-386 [doi:
10.1016/S0009-2614(01)00613-3]
Analysis of
Protein Structural Motifs in Terms of Sets of Codes Representing Local
Structures.
J. An, H. Wako & A. Sarai
Mol. Biol. (2001) 35, 905-910
[doi: 10.1023/A:1013250721578]
Significance of
a two-domain structure in subunits of phycobiliproteins
revealed by the normal mode analysis
H. Kikuchi, H. Wako, K. Yura, M. Go & M. Mimuro
Biophys. J. (2000) 79, 1587-1600 [abstract]
Construction of
an integrated environment for sequence, structure, property and function
analysis of proteins.
J. An, T. Nakama, Y. Kubota, H. Wako & A. Sarai
Genome Informatics (1999) 10, 229-230
[Full-text.pdf]
Novel method to
detect a motif of local structures in different protein conformations.
Wako, H. & Yamato, T.
Protein
A comparative
study of dynamic structures between phage 434 Cro and
repressor proteins by normal mode analysis.
Wako, H., Tachikawa, M. & Ogawa, A.
Proteins (1996) 26, 72-80 [abstract]
New
implementation of and the modeling by the extended simulated annealing process
to structures of T4 lysozyme mutants at the 86th
residue.
Endo, S., Higo, J., Nagayama, K. & Wako, H.
J. Comp. Chem. (1996) 17, 476-488 [abstract]
Conformational analysis of nucleic acid
molecules with flexible furanose rings in dihedral
angle space.
Tomimoto, M., Go, N. & Wako, H.
J. Comp. Chem. (1996) 17, 910-917 [abstract]
Secondary
structure prediction of β-subunits of the gonadotropin-thyrotropin
family from its aligned sequences using environment-dependent amino-acid
substitution tables and conformational propensities.
Wako. H. & Ishii, S.
Biochim. Biophys. Acta
(1995) 1247, 104-112 [abstract]
FEDER/2: program for static and dynamic
conformational energy analysis of macro-molecules in dihedral angle space.
Wako, H., Endo, S., Nagayama, K. & Go, N.
Comp. Phys. Comm. (1995) 19, 233-251 [abstract]
Dynamic
relationships among economic variables examined by the embedding method.
Inaba, T., Nagai, Y. & Wako, H.
Proceedings of the International Conference on Dynamical Systems and Chaos
Ed. Aoki N et al. (1995) World Scientific, Singapore,
381-388 [abstract]
The recognition of protein structure and
function from sequence: adding value to genome data.
May, A.C., Johnson, M.S.,
Philos. Trans. Roy. Soc. Lond. B Biol. Sci.
(1994) 344 373-381 [abstract]
Use of amino acid environment-dependent
substitution tables and conformational propensities in structure prediction
from aligned sequences of homologous proteins. II. Secondary structures.
Wako, H. & Blundell, T.L.
J. Mol. Biol. (1994) 238 693-708 [abstract]
Use of amino acid environment-dependent
substitution tables and conformational propensities in structure prediction
from aligned sequences of homologous proteins. I. Solvent accessibility
classes.
Wako, H. & Blundell, T.L.
J. Mol. Biol. (1994) 238 682-692 [abstract]
Molecular
biology of gonadotropins.
Ishii, S., Ando, H., Wako, H. & Kubota, Y.
Avian Endocrinology Ed. Sharp PJ (1993) J of Endocrinology
Ltd, Bristol, 123-134
A new version of
DADAS (Distance Analysis in Dihedral Angle Space) and its performance.
Endo, S., Wako, H., Nagayama, K. & Go, N.
Computational Aspects of the Study of Biological Macromoleculesby
Nuclear Magnetic Resonance Spectroscopy Ed. Hoch JC et al.
(1991) Plenum Press,
Distance-constraint
approach to higher-order structures of globular proteins with empirically
determined distances between amino acid residues.
Wako, H. & Kubota, Y.
J. Protein Chem. (1991) 10, 233-243 [abstract]
Protein
conformation in terms of conformational energy analysis.
Wako, H.
Protein Structural Analysis, Folding and Design Ed. HatanoH (1990) Japan Scientific Societies Press and
Elsevier, 3-17 [abstract]
A fractal model
of protein conformations and spectral exponents for the densities of
low-frequency normal modes of vibration.
Wako, H.
J. Phys. Soc. Jpn (1989) 58
1926-1929 [abstract]
Monte Carlo
simulations of a protein molecule with and without hydration energy calculated
by the hydration-shell model.
Wako, H.
J. Protein Chem. (1989) 8,
733-747 [abstract]
Dynamic structures of globular proteins
with respect to correlative movements of residues calculated in the normal mode
analysis.
Wako, H.
J. Protein Chem. (1989) 8 589-607 [abstract]
Inspection of
three-dimensional structures of proteins with dynamical information from the
normal mode analysis.
Wako, H.
Protein Seq. Data Anal. (1989) 2 175-180 [abstract]
Algorithm
for rapid calculation of hessian of conformational energy function of proteins by supercomputer.
Wako, H. & Go, N.
J. Comp. Chem. (1987) 8, 625-635. [abstract]
Development of
software tools for protein structure design.
Nakamura, N., Yamazaki, T., Abe, H., Noguchi, T., Seno, Y., Wako, H. & Go,
N.
J. Mol. Graph. (1986) 4, 180-181.
Unfolding of
tertiary structures of proteins.
Wakana, H., Yokomizo, H.,
Wako, H., Isogai, Y., Kosuge,
K. & Saito, N.
Int. J. Pept. Protein Res.
(1984) 23 657-670 [abstract]
Monte Carlo
study on local and small-amplitude conformational fluctuation in hen egg white lysozyme.
Wakana, H., Wako, H., & Saito, N.
Int. J. Pept. Protein Res. (1984) 23 315-323 [abstract]
Hydrophobic
interaction and the prediction of the tertiary structures of proteins.
Saito, N.,
Wako, H., Akutsu, T. & Oyama, Y.
In: Studies in Physical and Theoretical Chemistry (1983)
27, 325-338
Statistical
mechanical treatment of α-helices and extended structures in proteins with
inclusion of short- and medium-range interactions.
Wako, H., Saito, N. & Scheraga, H.A.
J. Protein Chem. (1983)
2, 221-249 [abstract]
Cis-trans
isomerization of proline in
the peptide (His 105-Val 124) of ribonuclease A
containing the primary nucleation site.
Mattew, R.P., Gerewitz, F., Wako, H. & Scheraga, H.A.
J. Protein Chem. (1983)
2, 131-146 [abstract]
Distance-constraint
approach to protein folding. II. Prediction
of three-dimensional structure of bovine pancreatic trypsin
inhibitor .
Wako, H. & Scheraga, H.A.
J. Protein Chem. (1982) 1, 85-117 [abstract]
Distance-constraint
approach to protein folding. I. Statistical
analysis of protein conformations in terms of distances between residues.
Wako, H. & Scheraga, H.A.
J. Protein Chem. (1982) 1, 5-45 [abstract]
Visualization of
the nature of protein folding by a study of a distance constraint approach in
two-dimensional models.
Wako, H. & Scheraga, H.A.
Biopolymers (1982) 21, 611-632 [abstract]
On the use of
distance constraints to fold a protein.
Wako, H. & Scheraga, H.A.
Macromolecules (1981) 14, 961-969 [abstract]
Statistical
mechanical theory of the protein conformation II. Folding pathway for protein.
Wako, H. & Saito, N.
J. Phys. Soc. Jpn (1978) 44,
1939-1945 [abstract]
Statistical
mechanical theory of the protein
Wako, H. & Saito, N.
J. Phys. Soc. Jpn (1978) 44,
1931-1938 [abstract]
Tertiary
structures of gastrin-like tetrapeptides.
Yamada, T., Wako, H., Saito, N., Isogai, Y. & Watari, H.
Int. J. Pept. Protein Res. (1976) 8
607-614 [abstract]
END
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