Kono H - Search Results

1

Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding.

Selvaraj S, Kono H, Sarai A. Selvaraj S, et al. Among authors: kono h. J Mol Biol. 2002 Oct 4;322(5):907-15. doi: 10.1016/s0022-2836(02)00846-x. J Mol Biol. 2002. PMID: 12367517

2

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

Gromiha MM, Oobatake M, Kono H, Uedaira H, Sarai A. Gromiha MM, et al. Among authors: kono h. Biopolymers. 2002 Aug 5;64(4):210-20. doi: 10.1002/bip.10125. Biopolymers. 2002. PMID: 12115138

3

Anatomy of specific interactions between lambda repressor and operator DNA.

Oobatake M, Kono H, Wang Y, Sarai A. Oobatake M, et al. Among authors: kono h. Proteins. 2003 Oct 1;53(1):33-43. doi: 10.1002/prot.10438. Proteins. 2003. PMID: 12945047

4

Intermolecular and intramolecular readout mechanisms in protein-DNA recognition.

Michael Gromiha M, Siebers JG, Selvaraj S, Kono H, Sarai A. Michael Gromiha M, et al. Among authors: kono h. J Mol Biol. 2004 Mar 19;337(2):285-94. doi: 10.1016/j.jmb.2004.01.033. J Mol Biol. 2004. PMID: 15003447

5

Integration of bioinformatics and computational biology to understand protein-DNA recognition mechanism.

Sarai A, Siebers J, Selvaraj S, Gromiha MM, Kono H. Sarai A, et al. Among authors: kono h. J Bioinform Comput Biol. 2005 Feb;3(1):169-83. doi: 10.1142/s0219720005000965. J Bioinform Comput Biol. 2005. PMID: 15751119

6

Protein-DNA recognition patterns and predictions.

Sarai A, Kono H. Sarai A, et al. Among authors: kono h. Annu Rev Biophys Biomol Struct. 2005;34:379-98. doi: 10.1146/annurev.biophys.34.040204.144537. Annu Rev Biophys Biomol Struct. 2005. PMID: 15869395 Review.

7

Role of inter and intramolecular interactions in protein-DNA recognition.

Gromiha MM, Siebers JG, Selvaraj S, Kono H, Sarai A. Gromiha MM, et al. Among authors: kono h. Gene. 2005 Dec 30;364:108-13. doi: 10.1016/j.gene.2005.07.022. Epub 2005 Oct 24. Gene. 2005. PMID: 16249059

8

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition.

Araúzo-Bravo MJ, Fujii S, Kono H, Ahmad S, Sarai A. Araúzo-Bravo MJ, et al. Among authors: kono h. J Am Chem Soc. 2005 Nov 23;127(46):16074-89. doi: 10.1021/ja053241l. J Am Chem Soc. 2005. PMID: 16287294

9

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

Ahmad S, Kono H, Araúzo-Bravo MJ, Sarai A. Ahmad S, et al. Among authors: kono h. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W124-7. doi: 10.1093/nar/gkl104. Nucleic Acids Res. 2006. PMID: 16844974 Free PMC article.

10

Sequence-dependent DNA deformability studied using molecular dynamics simulations.

Fujii S, Kono H, Takenaka S, Go N, Sarai A. Fujii S, et al. Among authors: kono h. Nucleic Acids Res. 2007;35(18):6063-74. doi: 10.1093/nar/gkm627. Epub 2007 Aug 30. Nucleic Acids Res. 2007. PMID: 17766249 Free PMC article.

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