3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules. - Jianghong An; T. Nakama; Y. Kubota; Akinori Sarai (Bioinform., 1998)

Methods for Predicting Target Sites of Transcription Factors. - Akinori Sarai (German Conference on Bioinformatics, 1999)

ProTherm: Thermodynamic Database for Proteins and Mutants. - M. Michael Gromiha; Jianghong An; Hidetoshi Kono; Motohisa Oobatake; Hatsuho Uedaira; Akinori Sarai (Nucleic Acids Res., 1999)

Multicanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction. - Kenji Sayano; Hidetoshi Kono; M. Michael Gromiha; Akinori Sarai (J. Comput. Chem., 2000)

ProTherm, version 2.0: thermodynamic database for proteins and mutants. - M. Michael Gromiha; Jianghong An; Hidetoshi Kono; Motohisa Oobatake; Hatsuho Uedaira; Ponraj Prabakaran; Akinori Sarai (Nucleic Acids Res., 2000)

ORI-GENE: gene classification based on the evolutionary tree. - Hideaki Mizuno; Yoshimasa Tanaka; Kenta Nakai; Akinori Sarai (Bioinform., 2001)

Thermodynamic database for protein-nucleic acid interactions (ProNIT). - Ponraj Prabakaran; Jianghong An; M. Michael Gromiha; Samuel Selvaraj; Hatsuho Uedaira; Hidetoshi Kono; Akinori Sarai (Bioinform., 2001)

ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another. - Julia V. Ponomarenko; Dagmara P. Furman; Anatoly S. Frolov; Nikolay L. Podkolodny; Galina Orlova; Mikhail P. Ponomarenko; Nikolay A. Kolchanov; Akinori Sarai (Nucleic Acids Res., 2001)

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. - Julia V. Ponomarenko; Tatyana I. Merkulova; Gennady V. Vasiliev; Zoya B. Levashova; Galina Orlova; Sergey V. Lavryushev; Oleg N. Fokin; Mikhail P. Ponomarenko; Anatoly S. Frolov; Akinori Sarai (Nucleic Acids Res., 2001)

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0. - M. Michael Gromiha; Hatsuho Uedaira; Jianghong An; Samuel Selvaraj; Ponraj Prabakaran; Akinori Sarai (Nucleic Acids Res., 2002)

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences. - Shandar Ahmad; M. Michael Gromiha; Akinori Sarai (Bioinform., 2003)

Structure-Function Relationship in DNA Sequence Recognition by Transcription Factors. - Akinori Sarai; Samuel Selvaraj; M. Michael Gromiha; Hidetoshi Kono (APBC, 2004)

Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information. - Shandar Ahmad; M. Michael Gromiha; Akinori Sarai (Bioinform., 2004)

Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. - Alexey V. Kochetov; Akinori Sarai (Bioinform., 2004)

ASAView: Database and tool for solvent accessibility representation in proteins. - Shandar Ahmad; M. Michael Gromiha; Hamed Fawareh; Akinori Sarai (BMC Bioinform., 2004)

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. - Shandar Ahmad; Akinori Sarai (Nucleic Acids Res., 2004)

ProTherm, version 4.0: thermodynamic database for proteins and mutants. - K. Abdulla Bava; M. Michael Gromiha; Hatsuho Uedaira; Koji Kitajima; Akinori Sarai (Nucleic Acids Res., 2004)

PSSM-based prediction of DNA binding sites in proteins. - Shandar Ahmad; Akinori Sarai (BMC Bioinform., 2005)

Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism. - Akinori Sarai; Jorg Siebers; Samuel Selvaraj; M. Michael Gromiha; Hidetoshi Kono (J. Bioinform. Comput. Biol., 2005)

The Diamond STING server. - Goran Neshich; Luiz C. Borro; Roberto H. Higa; Paula R. Kuser; Michel E. B. Yamagishi; Eduardo H. Franco; João N. Krauchenco; Renato Fileto; André A. Ribeiro; George B. P. Bezerra; Thiago M. Velludo; Tomás S. Jimenez; et al. (Nucleic Acids Res., 2005)

Disentangling the Role of Tetranucleotide in the Sequence-Dependence of DNA Conformation: A Molecular Dynamics Approach. - Marcos J. Araúzo-Bravo; Satoshi Fujii; Hidetoshi Kono; Akinori Sarai (APBC, 2006)

Dimensionality of amino acid space and solvent accessibility prediction with neural networks. - Marcos J. Araúzo-Bravo; Shandar Ahmad; Akinori Sarai (Comput. Biol. Chem., 2006)

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. - Shandar Ahmad; Hidetoshi Kono; Marcos J. Araúzo-Bravo; Akinori Sarai (Nucleic Acids Res., 2006)

ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. - M. D. Shaji Kumar; K. Abdulla Bava; M. Michael Gromiha; Ponraj Prabakaran; Koji Kitajima; Hatsuho Uedaira; Akinori Sarai (Nucleic Acids Res., 2006)

AUG_hairpin: prediction of a downstream secondary structure influencing the recognition of a translation start site. - Alexey V. Kochetov; Andrey Palyanov; Igor I. Titov; Dmitry A. Grigorovich; Akinori Sarai; Nikolay A. Kolchanov (BMC Bioinform., 2007)

Recognition of Drug-Target Interaction Patterns using Genetic Algorithm-optimized Bayesian-regularized Neural Networks and Support Vector Machines. - Michael Fernández; Akinori Sarai; Shandar Ahmad (SMC, 2009)

Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines. - Michael Fernández; Shandar Ahmad; Akinori Sarai (J. Chem. Inf. Model., 2010)

CCRXP: exploring clusters of conserved residues in protein structures. - Shandar Ahmad; Ozlem Keskin; Kenji Mizuguchi; Akinori Sarai; Ruth Nussinov (Nucleic Acids Res., 2010)

Prediction of dinucleotide-specific RNA-binding sites in proteins. - Michael Fernández; Yutaro Kumagai; Daron M. Standley; Akinori Sarai; Kenji Mizuguchi; Shandar Ahmad (BMC Bioinform., 2011)

Analysis of the relationships between evolvability, thermodynamics, and the functions of intrinsically disordered proteins/regions. - He Huang; Akinori Sarai (Comput. Biol. Chem., 2012)