S. Miyazawa

发表

Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

R. Jernigan, S. Miyazawa, 1985 .

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

R. Jernigan, S. Miyazawa, 1996, Journal of molecular biology.

An empirical energy potential with a reference state for protein fold and sequence recognition

R. Jernigan, S. Miyazawa, 1999, Proteins.

A reliable sequence alignment method based on probabilities of residue correspondences.

S. Miyazawa, 1995, Protein engineering.

Identifying sequence-structure pairs undetected by sequence alignments.

R L Jernigan, R. Jernigan, S. Miyazawa, 2000, Protein engineering.

A new substitution matrix for protein sequence searches based on contact frequencies in protein structures.

R. Jernigan, S. Miyazawa, Robert L Jernigan, 1993, Protein engineering.

Two types of amino acid substitutions in protein evolution

S. Miyazawa, T. Miyata, T. Yasunaga, 1979, Journal of Molecular Evolution.

Equilibrium folding and unfolding pathways for a model protein

R. Jernigan, S. Miyazawa, 1982, Biopolymers.

Selection originating from protein stability/foldability: Relationships between protein folding free energy, sequence ensemble, and fitness.

S. Miyazawa, 2016, Journal of theoretical biology.

Selection originating from protein foldability: II. Folding free energy, sequence ensemble, and fitness

S. Miyazawa, 2016 .

How effective for fold recognition is a potential of mean force that includes relative orientations between contacting residues in proteins?

Robert L Jernigan, Sanzo Miyazawa, R. Jernigan, 2005, The Journal of chemical physics.

Superiority of a mechanistic codon substitution model even for protein sequences in Phylogenetic analysis

S. Miyazawa, 2013, BMC Evolutionary Biology.

On the optimal contact potential of proteins

S. Miyazawa, A. Kinjo, 2007, 0709.0346.

Properties of contact matrices induced by pairwise interactions in proteins.

S. Miyazawa, A. Kinjo, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Numerical Evaluation of Biocide Treatment against Sulfate Reducing Bacteria in Oilfield Water Pipelines

S. Miyazawa, C. Inoue, K. Suto, 2007 .

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

S. Miyazawa, 2010, PloS one.

Protein sequence-structure alignment based on site-alignment probabilities.

S. Miyazawa, 2000, Genome informatics. Workshop on Genome Informatics.

Prediction of Residue-Contacts Based on Coevolution between Amino Acid Sites: Toward the Prediction of Protein Structure

S. Miyazawa, 2014 .

Stabilization of Regular Conformational Regions in Proteins by Intraregion Electrostatic Interactions

R. Jernigan, S. Miyazawa, S. Szu, 1980 .

Applications of Empirical Amino Acid Potential Functions

D. Covell, R. Jernigan, S. Miyazawa, 1995 .

Self‐consistent estimation of inter‐residue protein contact energies based on an equilibrium mixture approximation of residues

R. Jernigan, S. Miyazawa, 1999, Proteins.

Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences

Sanzo Miyazawa, S. Miyazawa, 2011, PloS one.

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

S. Miyazawa, 1985 .

Kerr Effects of Flexible Macromolecules

R. Jernigan, S. Miyazawa, 1981 .

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

Y. Kurosawa, S. Miyazawa, H. Hayashida, 1989, European journal of immunology.

Cooperative ligand binding on multidimensional lattices: Bethe approximation

S. Miyazawa, 1983 .

Selection maintaining protein stability at equilibrium.

S. Miyazawa, 2015, Journal of theoretical biology.

Relationship between mutability, polarity and exteriority of amino acid residues in protein evolution.

S. Miyazawa, M. Go, 2009, International journal of peptide and protein research.

Prediction of Structures and Interactions from Genome Information.

S. Miyazawa, 2017, Advances in experimental medicine and biology.

Prediction of Contact Residue Pairs Based on Co-Substitution between Sites in Protein Structures

Sanzo Miyazawa, S. Miyazawa, 2013, PloS one.

Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings From a Multiple Sequence Alignment

S. Miyazawa, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Inference of Co-Evolving Site Pairs: an Excellent Predictor of Contact Residue Pairs in Protein 3D structures

S. Miyazawa, 2012, 1208.1604.

Monte-Carlo Calculation of Quantum J 1 – J 2 Model on the Square Lattice

S. Miyazawa, S. Homma, 1995 .

Selection originating from protein foldability: I. A new method to estimate selection temperature

S. Miyazawa, 2016, 1612.09378.

Superiority of a mechanistic codon substitution model even for protein sequences in Phylogenetic analysis

S. Miyazawa, 2013, BMC Evolutionary Biology.

Volume and polarity changes accompanied by amino acid substitutions in protein evolution.

S. Miyazawa, M. Go, 2009, International journal of peptide and protein research.

Evaluation of short‐range interactions as secondary structure energies for protein fold and sequence recognition

Sanzo Miyazawa, R. Jernigan, S. Miyazawa, 1999, Proteins.

Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings From a Multiple Sequence Alignment

S. Miyazawa, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.