Refereed publications


  1. Miyazawa, Sanzo:
    Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings from a Multiple Sequence Alignment.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19, 328-342, 2022.
    doi:10.1109/TCBB.2020.2993232 (published in 2020) |
    The latest version including corrections: arXiv:1909.05006 [q-bio.BM], 2024.
    arXiv Preprint server: arXiv:1909.05006 [q-bio.BM], 2019; Errors corrected, 2024.
    A program written in scala and data employed: GitLab | Code Ocean (DOI: 10.24433/CO.9245367.v1)

  2. Miyazawa, Sanzo:
    Prediction of Structures and Interactions from Genome Information
    In: H. Nakamura (ed.) Integrative Structural Biology with Hybrid Methods, Advances in Experimental Medicine and Biology 1105, chap. 9.
    Springer Nature Singapore Pte Ltd. (2018).
    DOI 10.1007/978-981-13-2200-6_9
    arXiv preprint server: arXiv:1709.08021 [q-bio.BM], 2017 | PDF for the full version of the appendix.

  3. Miyazawa, Sanzo:
    Selection originating from protein stability/foldability: Relationships between protein folding free energy, sequence ensemble, and fitness.
    J. Theor. Biol., 433, 21-38, 2017.
    doi:10.1016/j.jtbi.2017.08.018 | Full text (HTML) | Full text (pdf)
    Supplementary files: Supplementary file 1 (pdf)
    The latest version including corrections: arXiv:1612.09379 [q-bio.BM], 2024.
    arXiv Preprint server: arXiv:1612.09379 [q-bio.BM], 2016; Errors corrected, 2024.

  4. Miyazawa, Sanzo:
    Selection maintaining protein stability at equilibrium.
    Autoslides at elsevier.com | Slides (pdf)
    J. Theor. Biol., 391, 21-34, 2016.
    doi:10.1016/j.jtbi.2015.12.001
    Full text (HTML) | Full text (pdf)
    Supplementary files: Supplementary file 1 (pdf) | Supplementary file 2 (dG.dat) | Supplementary file 3 (dG_vs_ddG.dat)
    arXiv Preprint server: arXiv:1512.08913 [q-bio.BM], 2015

  5. Miyazawa, Sanzo:
    Prediction of Residue-Contacts Based on Coevolution between Amino Acid Sites: Toward the Prediction of Protein Structure.
    Seibutsu-Butsuri, 54, (2), 91-95, 2014. In Japanese.
    doi:10.2142/biophys.54.091 | https://www.jstage.jst.go.jp/article/biophys/54/2/54_091/_article/
    Full text (pdf) | Supplement (pdf)

  6. Miyazawa, Sanzo:
    Superiority of a Mechanistic Codon Substitution Model Even for Protein Sequences in Phylogenetic Analysis.
    doi:10.1186/1471-2148-13-257 | http://www.biomedcentral.com/1471-2148/13/257
    BMC Evol. Biol., 13, 257, 2013.
    doi:10.1186/1471-2148-13-257 | http://www.biomedcentral.com/1471-2148/13/257
    Full text (pdf)
    Additional file 1: additional file 1 (pdf)

  7. Miyazawa, Sanzo: Prediction of contact residue pairs based on co-substitution between sites in protein structures.
    PLoS One, 8, e54252/pp. 1-20, 2013.
    doi:10.1371/journal.pone.0054252
    Full text (pdf) | Errata (pdf)
    Supporting Information: Figures S1-S6 and Table S1 (tar bz2 file) | Data S1 (tar bz2 file)
    arXiv Preprint server: arXiv:1208.1604 [q-bio.BM], 2012

  8. Miyazawa, Sanzo:
    Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.
    PLoS One, 6, e28892/pp. 1-20, 2011.
    doi:10.1371/journal.pone.0028892
    Full text (pdf)

  9. Miyazawa, Sanzo:
    Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes.
    PLoS One, 6, e17244/pp. 1-22, 2011.
    doi:10.1371/journal.pone.0017244
    Full text (pdf) | Errata (pdf)
    Supporting Information: text_s1.pdf | data_s1.txt
    arXiv Preprint server: arXiv:1004.5465 [q-bio.BM], 2010

  10. Miyazawa, Sanzo and Kinjo, Akira R.:
    Properties of contact matrices induced by pairwise interactions in proteins.
    Physical Review E, 77, 051910/pp. 1-10, 2008.
    Virtual Journal of Biological Physics Research, Vol. 15, Issue 10, May 15, 2008.
    doi:10.1103/PhysRevE.77.051910
    Full text (pdf) | Errata (pdf)
    arXiv Preprint server: arXiv:0801.0365 [q-bio.BM], 2008

  11. Kinjo, Akira R. and Miyazawa, Sanzo:
    On the optimum contact potential of proteins.
    Chemical Physics Letters, 451, 132-135, 2008.
    doi:10.1016/j.cplett.2007.12.005
    Full text (pdf)

  12. Vilcaez, J., Miyazawa, S., Suto, K., and Inoue, C.:
    Numerical evaluation of biocide treatment against sulfate reducing bacteria in oilfield water pipelines.
    Journal of the Japan Petroleum Institute, 50, 208-217, 2007.
    doi:10.1627/jpi.50.208

  13. Miyazawa, Sanzo and Jernigan, Robert L.:
    How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?
    Journal of Chemical Physics, 122, 024901, 2005.
    doi:10.1063/1.1824012
    Abstract | Full text (pdf) | Tables in EPAPS (pdf)
    Orientaional distributions compiled from protein structures

  14. Miyazawa, Sanzo and Jernigan, Robert L.:
    Long- and short-range interactions in native protein structures are consistent/minimally frustrated in sequence space.
    PROTEINS: Structures, Function, and Genetics, 50, 35-43, 2003.
    doi:10.1002/prot.10242
    Abstract | Full text (pdf)
    Cited by 6 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 5 papers in Google Scholar by 2005/06/15.

  15. Miyazawa, Sanzo:
    Protein sequence-structure alignment based on site-alignment probabilities.
    Genome Informatics, 11, 141-150, 2000.
    doi:10.11234/gi1990.11.141
    Abstract | Full text (pdf)

  16. Miyazawa, Sanzo and Jernigan, Robert L.:
    Identifying sequence-structure pairs undetected by sequence alignments.
    Protein Engineering, 13, 459-475, 2000.
    doi:10.1093/protein/13.7.459
    Abstract | Full text (pdf) | Errata (pdf)
    Cited by 9 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 10 papers in Google Scholar by 2005/06/15.

  17. Miyazawa, Sanzo and Jernigan, Robert L.:
    An Empirical Energy Potential with a Reference State for Protein Fold and Sequence Recognition.
    PROTEINS: Structures, Function, and Genetics, 36, 357-369, 1999.
    doi:10.1002/(SICI)1097-0134(19990815)36:3<357::AID-PROT10>3.0.CO;2-U
    Abstract | Full text (pdf) | Errata (pdf)
    Cited by 26 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 24 papers in Google Scholar by 2005/06/15.

  18. Miyazawa, Sanzo and Jernigan, Robert L.:
    Evaluation of Short-Range Interactions as Secondary Structure Energies for Protein Fold and Sequence Recognition.
    PROTEINS: Structures, Function, and Genetics, 36, 347-356, 1999.
    doi:10.1002/(SICI)1097-0134(19990815)36:3<347::AID-PROT9>3.0.CO;2-3
    Abstract | Full text (pdf)
    Cited by 18 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 14 papers in Google Scholar by 2005/06/15.

  19. Miyazawa, Sanzo and Jernigan, Robert L.:
    Self-consistent Estimation of Inter-residue Protein Contact Energies Based on an Equilibrium Mixture Approximation of Residues.
    PROTEINS: Structures, Function, and Genetics, 34, 49-68, 1999.
    doi:10.1002/(SICI)1097-0134(19990101)34:1<49::AID-PROT5>3.0.CO;2-L
    Abstract | Full text (pdf)
    Cited by 33 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 27 papers in Google Scholar by 2005/06/15.

  20. Miyazawa, Sanzo:
    Empirical Inter-residue potentials for Protein Structures,
    Butsuri, 52, 312-319, 1997. In Japanese.
    doi:10.11316/butsuri1946.52.312
    Abstract | Draft (pdf) | Reprint (pdf)

  21. Miyazawa, Sanzo and Jernigan, Robert L.:
    Residue-Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term for Simulation and Threading.
    Journal of Molecular Biology., 256, 623-644, 1996.
    doi:10.1006/jmbi.1996.0114
    Abstract | Full text (pdf)
    Cited by 295 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 245 papers in Google Scholar by 2005/06/15.

  22. Miyazawa, Sanzo:
    A Reliable Sequence Alignment Method based on Probabilities of Residue Correspondences.
    Protein Engineering, 8, 999-1009, 1995.
    doi:10.1093/protein/8.10.999
    Abstract | Full text | Errata (pdf)
    Cited by 6 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 16 papers in Google Scholar by 2005/06/15.

  23. Jernigan, R. L., Young, L., Covell, D. G., and Miyazawa, Sanzo:
    Applications of Empirical Amino Acid Potential Functions.
    In: Modelling of Biomolecular Structures and Mechanisms, eds. Pullman, A. et al., Kluwer Academic Publishers, pp. 151-166, 1995.
    doi:10.1007/978-94-011-0497-5_13
    Full text (pdf)
    Cited by 1 papers in Thomson Science Citation Index by 2005/06/15.

  24. Miyazawa, S. and Honma, S.:
    Monte Carlo Calculation of Quantum J1 - J2 Model on the Square Lattice.
    In: Springer Proceedings in Physics, Vol. 80; Computer Simulation Studies in Condensed Matter Physics VIII, Recent Developments. Eds. Landau, D. P., Mon, K. K., and Schuttler, H. B., Tokyo: Springer Verlag, pp.78-88, 1995.
    (Proceedings of the Eighth Workshop, Athens, GA, USA, February 20-24, 1995.)
    doi:10.1007/978-3-642-79991-4_8
    Full text (pdf)
    Cited by 1 papers in Thomson Science Citation Index by 2005/06/15.

  25. Miyazawa, S. and Honma, S.:
    Monte Carlo Calculation of the Quantum J1-J2 Model on the Square Lattice.
    Physics Letters A, 193, 370-374, 1994.
    doi:10.1016/0375-9601(94)90967-9
    Full text (pdf)
    Cited by 4 papers in Thomson Science Citation Index by 2005/06/15.

  26. Miyazawa, Sanzo and Jernigan, Robert L.:
    Protein Stability for Single Substitutions Mutants and the Extent of Lacal Compactness in the Denatured State,
    Protein Engineering, 7, 1209-1220, 1994.
    doi:10.1093/protein/7.10.1209
    Abstract | Full text (pdf)
    Cited by 35 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 23 papers in Google Scholar by 2005/06/15.

  27. Miyazawa, S., Miyashita, S., Makivic, M., and Honma, S.:
    A Modified Decoupled Cell Method of Quantum Monte Carlo Calculation.
    Progress of Theoretical Physics, 89, 1167-1173, 1993.
    doi:10.1143/ptp/89.6.1167
    Full text (pdf)
    Cited by 5 papers in Thomson Science Citation Index by 2005/06/15.

  28. Miyazawa, Sanzo and Jernigan, Robert L.:
    A New Substitution Matrix for Protein Sequence Searches Based on Contact Frequencies in Protein Structures.
    Protein Engineering, 6, 267-278, 1993.
    doi:10.1093/protein/6.3.267
    Abstract | Full text (pdf)
    Cited by 29 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 18 papers in Google Scholar by 2005/06/15.

  29. Miyazawa, S., Makivic, M., Horiki, T. and Honma, S.:
    Numerical Experiments on Frustrated Quantum Spin Systems.
    In: Computaional Approach in Condensed Matter Phenomena, (Proceedings of 6th Nishinomiya-Yukawa Memorial Symposium, Nishinomiya, Japan, Oct. 24-25, 1991), 168-170, 1992, Tokyo: Springer Verlag.
    doi:10.1007/978-3-642-84821-6_27
    Full text (pdf)

  30. Miyauchi, T., Kanekura, T., Yamaoka, A., Ozawa, M., Miyazawa, S. and Muramatsu, T.:
    Basigen, a New, Broadly Distributed Member of the Immunoglobulin Superfamily, has Strong Homology with Both the Immunoglobulin V Domain and Beta-chain of Major Histocompatibility Complex Class II Antigen.
    Journal of Biochemistry, 107, 316-323, 1990.
    doi:10.1093/oxfordjournals.jbchem.a123045
    Full text (pdf)
    Cited by 83 papers in Thomson Science Citation Index by 2005/06/15.

  31. Miyazawa, Sanzo:
    DNA Data Bank of Japan: Present Status and Future Plans.
    In: Computers and DNA, Santa Fe Institute Studies in the Sciences of Complexity. vol. VII, Eds. G. I. Bell and T. G. Marr, Reading MA: Addison-Wesley, pp.47-61, 1990, (selected paper). ISBN-13: 978-0201515053
    Full text (pdf)
    Cited by 5 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 2 papers in Google Scholar by 2005/06/15.

  32. Ichihara, Y., Hayashida, H. Miyazawa, S., and Kurosawa, Y.
    Only Dfl16, Dsp2, and Dq52 gene families exist in mouse immunoglobulin heavy chain diversity gene loci, of which Dfl16 and Dsp2 originate from the same primordial Dh gene
    European Journal of Immunology, 19, 1849-1854, 1989.
    doi:10.1002/eji.1830191014
    Full text (pdf)

  33. Miyazawa, Sanzo:
    Statistical Mechanics of Supercoiling-Induced B-to-Z Transitions in a Closed Circular DNA: One-Dimensional Model System with A double Quadratic Displacement Potential and Long Range Interactions.
    Journal of Chemical Physics, 83, 859-883, 1985.
    doi:10.1063/1.449502
    Abstract | Full text (pdf) | Full text (pdf of scanned images)
    Cited by 3 papers in Thomson Science Citation Index by 2005/06/15.

  34. Miyazawa, Sanzo and Jernigan, Robert L.:
    Estimation of Effective Interresidue Contact Energies in Protein Crystal Structures: Quasi-Chemical Approximation.
    Macromolecules, 18, 534-552, 1985.
    doi:10.1021/ma00145a039
    Full text (pdf) | Full text (pdf of scanned images)
    Top 10th most cited until 2006 in Macromolecule. (PDF)
    Cited by 606 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 389 papers in Google Scholar by 2005/06/15.

  35. Miyazawa, Sanzo:
    Cooperative Ligand Binding on Multi-Dimensional Lattices: Bethe Approximation.
    Biopolymers, 22, 2253-2271, 1983.
    doi:10.1002/bip.360221010
    Full text (pdf)
    Cited by 6 papers in Thomson Science Citation Index by 2005/06/15.

  36. Jernigan, R. L. and Miyazawa, Sanzo:
    Equilibrium Folding-Unfolding Pathways of Model Proteins: Effects of Myoglobin Heme Contacts.
    Biopolymers, 22, 79-85, 1983.
    doi:10.1002/bip.360220113
    Full text (pdf)
    Cited by 2 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 1 papers in Google Scholar by 2005/06/15.

  37. Miyazawa, Sanzo and Jernigan, Robert L.:
    Equilibrium Folding Pathways for Model Proteins.
    Journal of Statistical Physics, 30, 549-559, 1983.
    doi:10.1007/BF01012328
    Full text (pdf)
    Cited by 2 papers in Thomson Science Citation Index by 2005/06/15.

  38. Miyazawa, Sanzo and Jernigan, Robert L.:
    Most Probable Intermediates in Protein Folding-Unfolding with a Non-Interacting Globule-Coil Model.
    Biochemistry, 21, 5203-5213, 1982.
    doi:10.1021/bi00264a015
    Full text (pdf)
    Cited by 11 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 2 papers in Google Scholar by 2005/06/15.

  39. Miyazawa, Sanzo and Jernigan, Robert L.:
    Equilibrium Folding and Unfolding Pathways for a Model Protein.
    Biopolymers, 21, 1333-1363, 1982.
    doi:10.1002/bip.360210706
    Full text (pdf)
    Cited by 26 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 6 papers in Google Scholar by 2005/06/15.

  40. Jernigan, R. L. and Miyazawa, Sanzo:
    Kerr Effects of Flexible Macromolecules.
    In: Molecular Electro-Optics, Electro-Optic Properties of Macromolecules and Colloids in Solution, ed. Sonja Krause, New York: Plenum Press, pp. 163-179, 1981, (selected paper).
    doi:10.1007/978-1-4684-3914-4_8
    Full text (pdf)
    Cited by 5 papers in Thomson Science Citation Index by 2005/06/15.

  41. Jernigan, R. L., Miyazawa, S. and Szu, S. C.:
    Electrostatic Interactions and Secondary Structures in Proteins.
    Biophysical Journal, 32, 93-95, 1980.
    doi:10.1016/S0006-3495(80)84926-5
    Full text (pdf)

  42. Jernigan, R. L., Miyazawa, S. and Szu, S. C.:
    Stabilization of Regular Conformational Regions in Proteins by Intra-region Electrostatic Interactions.
    Macromolecules, 13, 518-525, 1980.
    doi:10.1021/ma60075a010
    Full text (pdf)
    Cited by 10 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 2 papers in Google Scholar by 2005/06/15.

  43. Go, M. and Miyazawa, Sanzo:
    Relationship between Mutability, Polarity and Exteriority of Amino Acid Residues in Protein Evolution. International
    Journal of Peptide and Protein Research, 15, 211-224, 1980.
    doi:10.1111/j.1399-3011.1980.tb02570.x
    Full text (pdf)
    Cited by 64 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 8 papers in Google Scholar by 2005/06/15.

  44. Miyata, T., Miyazawa, S. and Yasunaga, T.:
    Two Types of Amino Acid Substitutions in Protein Evolution.
    Journal of Molecular Evolution, 12, 219-236, 1979.
    doi:10.1007/BF01732340
    Full text (pdf)
    Cited by 170 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 94 papers in Google Scholar by 2005/06/15.

  45. Go, M. and Miyazawa, Sanzo:
    Volume and Polarity Changes Accompanied by Amino Acid Substitutions in Protein Evolution.
    International Journal of Peptide and Protein Research, 12, 237- 241, 1978.
    doi:10.1111/j.1399-3011.1978.tb02893.x
    Full text (pdf)
    Cited by 5 papers in Thomson Science Citation Index by 2005/06/15.
    Cited by 1 papers in Google Scholar by 2005/06/15.

  46. Go, M. and Miyazawa, Sanzo:
    Relationship between Mutability and Location of Amino Acid Residues in the Three-dimensional Structure of Proteins.
    In: Evolution of Protein Molecules, eds. H. Matsubara and T. Yamanaka, Tokyo: Center for Academic Publications Japan, pp. 33-43, 1978, (selected paper).
    Full text (pdf)

  47. Go, N., Mizuno, H., Go, M., Miyazawa, S. and Taketomi, H.:
    Protein Atomic Coordinate Data and Their Information Processing.
    Protein, Nucleic Acid and Enzyme, 23, 1336-1344, 1978, in Japanese.
    Full text (pdf)