Publications


ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins.
Wako, H. and Endo, S.
The Open Bioinformatics Journal, (2012) 6, 9-19.  [doi:10.2174/1875036201206010009]


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, S.
Bioinformatics
(2004) 20,  2035-2043    [doi: 10.1093/bioinformatics/bth197]

    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 -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 Monte Carlo method in protein simulation
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 Eng. (1998) 11,  981-990    [abstract]


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 -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., Rufino, S.D., Wako, H., Zhu, Z.Y., Sowdhamini, R., Srinivasan,N., Rodionov, M.A. & Blundell, T.L.
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, New York, 233-251   [abstract]



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  [doi: 10.1143/JPSJ.58.1926]



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 -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  [doi: 10.1021/ma50005a014]



Statistical mechanical theory of the protein conformation II. Folding pathway for protein.
Wako, H. & Saito, N.
J. Phys. Soc. Jpn (1978)  44,  1939-1945  [doi: 10.1143/JPSJ.44.1939]



Statistical mechanical theory of the protein conformation I. General considerations and the application to homopolymers.
Wako, H. & Saito, N.
J. Phys. Soc. Jpn (1978)  44,  1931-1938  [doi: 10.1143/JPSJ.44.1931]



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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