A. Sarai

Huajian Gao, A. Sarai, T. Gao, 2004, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines

Shandar Ahmad, Akinori Sarai, Michael Fernández, 2010, J. Chem. Inf. Model..

Negative autoregulation of c-Myb activity by homodimer formation through the leucine zipper.

A. Sarai, S. Ishii, T. Gonda, 1993, The Journal of biological chemistry.

Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast.

H. Kono, A. Sarai, M. Fernández, 2009, Genome informatics. International Conference on Genome Informatics.

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition

Shandar Ahmad, Akinori Sarai, Marcos J. Araúzo-Bravo, 2006, Nucleic Acids Res..

Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach

Akinori Sarai, Marcos J. Araúzo-Bravo, Satoshi Fujii, 2006, APBC.

Knowledge-based prediction of DNA atomic structure from nucleic sequence.

Marcos J Araúzo-Bravo, Akinori Sarai, M. Araúzo-Bravo, 2005, Genome informatics. International Conference on Genome Informatics.

The role of alternative translation start sites in the generation of human protein diversity

Nikolay A. Kolchanov, Igor B. Rogozin, Alex V. Kochetov, 2005, Molecular Genetics and Genomics.

Unique Mode of GCC Box Recognition by the DNA-binding Domain of Ethylene-responsive Element-binding Factor (ERF Domain) in Plant*

A. Sarai, M. Ohme-Takagi, Dongyun Hao, 1998, The Journal of Biological Chemistry.

Thermodynamics of specific and non-specific DNA binding by the c-Myb DNA-binding domain.

K Furukawa, A. Sarai, H. Nakamura, 1998, Journal of molecular biology.

ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions

Akinori Sarai, M. Michael Gromiha, M. D. Shaji Kumar, 2005, Nucleic Acids Res..

Solvent density and long‐range dipole field around a DNA‐binding protein studied by molecular dynamics

H. Kono, A. Sarai, J. Higo, 2000, Proteins.

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information

Shandar Ahmad, Akinori Sarai, M. Michael Gromiha, 2004, Bioinform..

Lambda repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically.

A. Sarai, A Sarai, Y. Takeda, 1989, Proceedings of the National Academy of Sciences of the United States of America.

AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site

Akinori Sarai, Nikolay A. Kolchanov, Alexey V. Kochetov, 2007, BMC Bioinformatics.

Bending of DNA by IHF Protein

R. Jernigan, A. Sarai, S. Goodman, 1990 .

Binding site analysis of c-Myb: screening of potential binding sites by using the mutation matrix derived from systematic binding affinity measurements.

A. Sarai, S. Ishii, Q. Deng, 1996, Nucleic acids research.

DNA fingerprinting involving fluorescence-labeled termini of any enzymatically generated fragments of DNA

A. Sarai, K. Yokoyama, Xiaoren Tang, 1994, Japanese Journal of Human Genetics.

PSSM-based prediction of DNA binding sites in proteins

Shandar Ahmad, Akinori Sarai, A. Sarai, 2005, BMC Bioinformatics.

Distinct patterns in homooligomer tract sequence context in prokaryotic and eukaryotic DNA.

R Nussinov, R L Jernigan, R. Nussinov, 1989, Biochimica et biophysica acta.

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences

Shandar Ahmad, Akinori Sarai, M. Michael Gromiha, 2003, Bioinform..

NF-E2 p45 Is Important for Establishing Normal Function of Platelets

H. Aburatani, A. Sarai, E. Bresnick, 2013, Molecular and Cellular Biology.

Hydrophobic interactions in the major groove can influence DNA local structure.

R. Nussinov, R. Jernigan, A. Sarai, 1986, Journal of biomolecular structure & dynamics.

Prediction of dinucleotide-specific RNA-binding sites in proteins

Shandar Ahmad, Kenji Mizuguchi, Akinori Sarai, 2011, BMC Bioinformatics.

Kinetic analysis of DNA binding by the c‐Myb DNA‐binding domain using surface plasmon resonance

K Furukawa, A. Sarai, H. Nakamura, 1999, FEBS letters.

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

A. Sarai, F. Pichierri, 1999 .

Energy-gap and temperature dependence of electron and excitation transfer in biological systems

A. Sarai, 1979 .

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

Akinori Sarai, Anatoly S. Frolov, Tatyana I. Merkulova, 2001, Nucleic Acids Res..

Importance of mutant position in Ramachandran plot for predicting protein stability of surface mutations.

M Michael Gromiha, Hidetoshi Kono, Akinori Sarai, 2002, Biopolymers.

A model of the strain-induced B-Z transition.

R. Jernigan, A. Sarai, 1985, Journal of Biomolecular Structure and Dynamics.

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins

Shandar Ahmad, Akinori Sarai, A. Sarai, 2004, Nucleic Acids Res..

Self-consistent evaluation of static solitons, pinning energy and soliton energy in discrete one-dimensional soliton models

A. Sarai, 1986 .

Stress-induced nonlinear structural transition in DNA

A. Sarai, 1984 .

Free energy calculations for the relative binding affinity between DNA and λ‐repressor

Akinori Sarai, Minoru Saito, A. Sarai, 2003 .

The mutant RecA proteins, RecAR243Q and RecAK245N, exhibit defective DNA binding in homologous pairing.

A. Sarai, T. Shibata, H. Kurumizaka, 1999, Archives of biochemistry and biophysics.

ORI-GENE: gene classification based on the evolutionary tree

Kenta Nakai, Akinori Sarai, Yoshimasa Tanaka, 2001, Bioinform..

Conformational Effects of DNA Stretching

R. Jernigan, A. Sarai, J. Mazur, 2003, Molecular Biology.

Theoretical studies on the interaction of proteins with base pairs. II: Effect of external H- bond interactions on the stability of guanine-cytosine and non Watson-Crick pairs

A. Sarai, M. Saito, 1985 .

Structure-Thermodynamic Relationship in Protein-DNA Binding: Heat Capacity Changes

Akinori Sarai, Hatsuho Uedaira, Koji Kitajima, 2003 .

Moment-based prediction of DNA-binding proteins.

Akinori Sarai, A. Sarai, Shandar Ahmad, 2004, Journal of molecular biology.

ProTherm: Thermodynamic Database for Proteins and Mutants

Akinori Sarai, M. Michael Gromiha, Jianghong An, 1999, Nucleic Acids Res..

Comment on ‘‘IR‐spectroscopic study of isotope effects on the NH/ND stretching bands of meso‐tetraphenylporphine and vibrational hydrogen tunneling’’

A. Sarai, 1984 .

Filling a cavity dramatically increases pressure stability of the c‐Myb R2 subdomain

A. Sarai, H. Morii, K. Ogata, 2001, Proteins.

Identification of indispensable residues for specific DNA-binding in the imperfect tandem repeats of c-Myb R2R3.

K Furukawa, A. Sarai, H. Nakamura, 1997, Protein engineering.

Recognition of drug-target interaction patterns using genetic algorithm-optimized Bayesian-regularized neural networks and support vector machines

Shandar Ahmad, Akinori Sarai, Michael Fernández, 2009, 2009 IEEE International Conference on Systems, Man and Cybernetics.

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0

Akinori Sarai, M. Michael Gromiha, Jianghong An, 2002, Nucleic Acids Res..

Multi-state thermal transitions of proteins - DNA-binding domain of the c-Myb oncoprotein

A. Sarai, S. Ishii, H. Morii, 1998 .

ProTherm, version 4.0: thermodynamic database for proteins and mutants

Akinori Sarai, Hatsuho Uedaira, Koji Kitajima, 2004, Nucleic Acids Res..

Sequence dependence of the B‐A conformational transition of DNA

R. Jernigan, A. Sarai, J. Mazur, 1989, Biopolymers.

Thermodynamic databases for proteins and protein-nucleic acid interactions.

P Prabakaran, M. Gromiha, M. Oobatake, 2001, Biopolymers.

ProTherm, version 2.0: thermodynamic database for proteins and mutants

Akinori Sarai, M. Michael Gromiha, Jianghong An, 2000, Nucleic Acids Res..

ProTherm, Thermodynamic database for proteins and mutants.

M. Gromiha, M. Oobatake, H. Kono, 1999 .

Automatic Construction of Search Condition for Making an Exhaustive List of Similar Papers

Akinori Sarai, Jianghong An, Takao Nakama, 2000 .

Missense mutations in the Bacillus subtilis gnt repressor that diminish operator binding ability.

A. Sarai, Y. Fujita, K. Yoshida, 1993, Journal of molecular biology.

Relationship between curved DNA conformations and slow gel migration.

R. Nussinov, R. Jernigan, A. Sarai, 1987, Journal of biomolecular structure & dynamics.

Shape and energetics of a cavity in c-Myb probed by natural and non-natural amino acid mutations.

A. Sarai, S. Ishii, H. Morii, 1999, Journal of molecular biology.

Solution structures of Myb DNA-binding domain and its complex with DNA.

A. Sarai, S. Ishii, M. Sasaki, 1993, Nucleic acids symposium series.

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

Shandar Ahmad, Akinori Sarai, Marcos J. Araúzo-Bravo, 2006, Comput. Biol. Chem..

Thermodynamic database for proteins: features and applications.

Akinori Sarai, M Michael Gromiha, M. Gromiha, 2010, Methods in molecular biology.

Systematic single base‐pair substitution analysis of DNA binding by the cAMP receptor protein in cyanobacterium Synechocystis sp. PCC 6803

A. Suyama, A. Sarai, M. Takano, 2004, FEBS letters.

Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism

Akinori Sarai, M. Michael Gromiha, Samuel Selvaraj, 2005, J. Bioinform. Comput. Biol..

Thermodynamic database for protein-nucleic acid interactions (ProNIT)

Akinori Sarai, M. Michael Gromiha, Jianghong An, 2001, Bioinform..

Construction of an artificial tandem protein of the c-Myb DNA-binding domain and analysis of its DNA binding specificity.

A. Sarai, H. Nakamura, K. Furukawa, 1999, Biochemical and biophysical research communications.

DNA-Protein Interactions: Target Prediction

H. Kono, A. Sarai, 2004 .

Multicanonical Monte Carlo calculation of the free‐energy map of the base–amino acid interaction

M. Michael Gromiha, Hidetoshi Kono, Akinori Sarai, 2000 .

Prediction of DNA Target Sites by Regulatory Proteins.

H. Kono, A. Sarai, 2000 .

Prediction of DNA Target Sites by Regulatory Proteins Based on Structure-Derived Potential

H. Kono, A. Sarai, 1998 .

Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas.

S. Miyano, K. Kumamoto, J. Yokota, 2012, Cancer research.

Molecular dynamics study on mobility and dipole ordering of solvent around proteins: effects of periodic-box size and protein charge

Haruki Nakamura, Junichi Higo, Hiroki Shirai, 1999 .

MHC class II DR classification based on antigen-binding groove natural selection.

N. Saitou, A. Sarai, Y. Aida, 2009, Biochemical and biophysical research communications.

Solvation effects on the sequence variability of DNA double helical conformations.

R. Jernigan, A. Sarai, G. Raghunathan, 1990, Journal of biomolecular structure & dynamics.

Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana

Akinori Sarai, Alexey V. Kochetov, A. Sarai, 2004, Bioinform..

The Diamond STING server

Akinori Sarai, Renato Fileto, Goran Neshich, 2005, Nucleic Acids Res..

Cavity-Filling Mutations Enhance Protein Stability by Lowering the Free Energy of Native State

Hidetoshi Kono, Tahir H. Tahirov, Kazuhiro Ogata, 2000 .

PrognoScan: a new database for meta-analysis of the prognostic value of genes

K. Nakai, A. Sarai, K. Kitada, 2009, BMC Medical Genomics.

Contributory presentations/posters

Diederichs, Bosco K. Ho, Hironori K. Nakamura, 1999, Journal of Biosciences.

Analysis of Protein Structural Motifs in Terms of Sets of Codes Representing Local Structures

J. An, H. Wako, A. Sarai, 2004, Molecular Biology.

3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules

Akinori Sarai, Jianghong An, T. Nakama, 1998, Bioinform..

Interrelations between the efficiency of translation start sites and other sequence features of yeast mRNAs

N. A. Kolchanov, A. Sarai, A. Sarai, 2003, Molecular Genetics and Genomics.

CCRXP: exploring clusters of conserved residues in protein structures

Ozlem Keskin, Shandar Ahmad, Kenji Mizuguchi, 2010, Nucleic Acids Res..