| Year |
Citation |
Score |
| 2020 |
Negami T, Shimizu K, Terada T. Coarse-grained molecular dynamics simulation of protein conformational change coupled to ligand binding Chemical Physics Letters. 742: 137144. DOI: 10.1016/J.Cplett.2020.137144 |
0.361 |
|
| 2019 |
Fang C, Moriwaki Y, Li C, Shimizu K. MoRFPred_en: Sequence-based prediction of MoRFs using an ensemble learning strategy. Journal of Bioinformatics and Computational Biology. 17: 1940015. PMID 32019410 DOI: 10.1142/S0219720019400158 |
0.303 |
|
| 2019 |
Fang C, Moriwaki Y, Tian A, Li C, Shimizu K. Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method. Journal of Bioinformatics and Computational Biology. 17: 1950004. PMID 30866736 DOI: 10.1142/S0219720019500045 |
0.316 |
|
| 2016 |
Banno M, Komiyama Y, Cao W, Oku Y, Ueki K, Sumikoshi K, Nakamura S, Terada T, Shimizu K. Development of a sugar-binding residue prediction system from protein sequences using support vector machine. Computational Biology and Chemistry. 66: 36-43. PMID 27889654 DOI: 10.1016/J.Compbiolchem.2016.10.009 |
0.306 |
|
| 2016 |
Dawson WK, Jono R, Terada T, Shimizu K. Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center. Plos One. 11: e0162031. PMID 27656882 DOI: 10.1371/Journal.Pone.0162031 |
0.306 |
|
| 2016 |
Shigemitsu S, Cao W, Terada T, Shimizu K. Development of a prediction system for tail-anchored proteins. Bmc Bioinformatics. 17: 378. PMID 27634135 DOI: 10.1186/S12859-016-1202-7 |
0.311 |
|
| 2016 |
Tsujikawa H, Sato K, Wei C, Saad G, Sumikoshi K, Nakamura S, Terada T, Shimizu K. Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation. Journal of Structural and Functional Genomics. PMID 27400687 DOI: 10.1007/S10969-016-9204-2 |
0.34 |
|
| 2016 |
Terada T, Negami T, Shimizu K. A Multiscale Approach To Understanding Protein Ligand Binding Process Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.3437 |
0.314 |
|
| 2015 |
Yarimizu M, Wei C, Komiyama Y, Ueki K, Nakamura S, Sumikoshi K, Terada T, Shimizu K. Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine. Advances in Bioinformatics. 2015: 528097. PMID 26347773 DOI: 10.1155/2015/528097 |
0.305 |
|
| 2014 |
Negami T, Terada T, Shimizu K. 2P032 The factors determining protein-ligand binding processes revealed by comparative coarse-grained simulations(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54. DOI: 10.2142/Biophys.54.S200_2 |
0.343 |
|
| 2014 |
Moriwaki Y, Terada T, Caaveiro JMM, Tsumoto K, Shimizu K. 2P025 Structural insight into the heme-transfer mechanism between Isd proteins in Staphylococcus aureus(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54. DOI: 10.2142/Biophys.54.S199_1 |
0.329 |
|
| 2014 |
Terada T, Negami T, Shimizu K. 2SCP-05 Protein-ligand binding processes studied by coarse-grained molecular dynamics simulations(Prediction and analysis of protein functions from structural bioinformatics,Symposium,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014)) Seibutsu Butsuri. 54. DOI: 10.2142/Biophys.54.S133_1 |
0.364 |
|
| 2014 |
Moriwaki Y, Terada T, Caaveiro JM, Takaoka Y, Hamachi I, Tsumoto K, Shimizu K. Heme-Transfer Mechanism of Structurally Similar Isd NEAT Domains of Staphylococcus Aureus Exhibiting Different Affinities for Heme Biophysical Journal. 106: 660a. DOI: 10.1016/J.Bpj.2013.11.3653 |
0.308 |
|
| 2014 |
Negami T, Shimizu K, Terada T. Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Field Biophysical Journal. 106: 6-9. DOI: 10.1016/J.Bpj.2013.11.3370 |
0.305 |
|
| 2013 |
Moriwaki Y, Terada T, Caaveiro JM, Takaoka Y, Hamachi I, Tsumoto K, Shimizu K. Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of Staphylococcus aureus exhibiting different affinities for heme. Biochemistry. 52: 8866-77. PMID 24245481 DOI: 10.1021/Bi4008325 |
0.313 |
|
| 2013 |
Negami T, Terada T, Shimizu K. 2P044 Comparative simulations of protein-ligand binding processes using the MARTINI coarse-grained force field(01B. Protein: Structure & Function,Poster) Seibutsu Butsuri. 53. DOI: 10.2142/Biophys.53.S166_2 |
0.329 |
|
| 2012 |
Yamasaki S, Terada T, Kono H, Shimizu K, Sarai A. A new method for evaluating the specificity of indirect readout in protein-DNA recognition. Nucleic Acids Research. 40: e129. PMID 22618872 DOI: 10.1093/Nar/Gks462 |
0.318 |
|
| 2012 |
Negami T, Terada T, Shimizu K. 2PT133 Coarse-grained MD simulations of ligand binding to proteins : Effect of the conformational changes of the proteins(The 50th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 52. DOI: 10.2142/Biophys.52.S127_4 |
0.325 |
|
| 2012 |
Tsujikawa H, Umeda Y, Morita M, Nakamura S, Shimizu K. 2PT101 Protein-Ligand Binding Site Prediction by Using Energy-based Method with Amino Acid Conservation Scores(The 50th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 52. DOI: 10.2142/Biophys.52.S121_4 |
0.328 |
|
| 2011 |
Cao W, Sumikoshi K, Nakamura S, Terada T, Shimizu K. Prediction of N-myristoylation modification of proteins by SVM. Bioinformation. 6: 204-6. PMID 21738315 DOI: 10.6026/97320630006204 |
0.344 |
|
| 2011 |
Morita M, Terada T, Nakamura S, Shimizu K. BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states. Bmc Research Notes. 4: 143. PMID 21600047 DOI: 10.1186/1756-0500-4-143 |
0.321 |
|
| 2011 |
Nishimura A, Terada T, Nakamura S, Shimizu K. 1E1512 Protein tertiary structure prediction by multicanonical MD simulation with restraints based on secondary structure prediction(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51. DOI: 10.2142/Biophys.51.S40_6 |
0.335 |
|
| 2011 |
Ge Z, Cao W, Sumikoshi K, Nakamura S, Shimizu K. 1E1412 Development of a method for predicting carbohtdrate-binding proteins(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51: S40. DOI: 10.2142/Biophys.51.S40_2 |
0.308 |
|
| 2011 |
Negami T, Terada T, Shimizu K. 3D1012 Protein-ligand binding simulation with a coarse-graind force field, MARTINI(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 51. DOI: 10.2142/Biophys.51.S117_5 |
0.304 |
|
| 2010 |
Someya S, Kakuta M, Morita M, Sumikoshi K, Cao W, Ge Z, Hirose O, Nakamura S, Terada T, Shimizu K. Prediction of carbohydrate-binding proteins from sequences using support vector machines. Advances in Bioinformatics. PMID 20936154 DOI: 10.1155/2010/289301 |
0.34 |
|
| 2010 |
Jono R, Watanabe Y, Shimizu K, Terada T. Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment. Journal of Computational Chemistry. 31: 1168-75. PMID 19847783 DOI: 10.1002/Jcc.21401 |
0.305 |
|
| 2010 |
Terada T, Nishimura A, Shimizu K. 2P071 Generality of the protein structure prediction method based on molecular dynamics simulation with secondary structure information(The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50. DOI: 10.2142/Biophys.50.S94_4 |
0.369 |
|
| 2010 |
Nishimura A, Terada T, Shimizu K. 1P071 Protein tertiary structure prediction by folding simulation with secondary structure restraints(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50. DOI: 10.2142/Biophys.50.S31_5 |
0.36 |
|
| 2010 |
Nakamura S, Morita M, Kakuta M, Shimizu K. 3P297 Development of structure prediction server and model quality assessment platform for proteins(Bioinformatics: Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50. DOI: 10.2142/Biophys.50.S198_1 |
0.32 |
|
| 2010 |
Sumikoshi K, Nakamura S, Shimizu K. 3P016 Introducing intramolecular flexibility into protein-protein docking(Protein: Structure,The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50. DOI: 10.2142/Biophys.50.S147_4 |
0.334 |
|
| 2010 |
Ge Z, Cao W, Someya S, Kakuda M, Sumikoshi K, Terada T, Nakamura S, Shimizu K. 2P295 Development of a method for predicting carbohydrate-binding proteins(The 48th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 50: S134-S135. DOI: 10.2142/Biophys.50.S134_7 |
0.327 |
|
| 2009 |
Cao W, Maruyama J, Kitamoto K, Sumikoshi K, Terada T, Nakamura S, Shimizu K. Using a new GPI-anchored-protein identification system to mine the protein databases of Aspergillus fumigatus, Aspergillus nidulans, and Aspergillus oryzae. The Journal of General and Applied Microbiology. 55: 381-93. PMID 19940384 DOI: 10.2323/Jgam.55.381 |
0.331 |
|
| 2009 |
Yamasaki S, Terada T, Shimizu K, Kono H, Sarai A. A generalized conformational energy function of DNA derived from molecular dynamics simulations. Nucleic Acids Research. 37: e135. PMID 19729512 DOI: 10.1093/Nar/Gkp718 |
0.343 |
|
| 2009 |
Ikezawa H, Morita M, Shimizu K. 1P-015 Development of protein-ligand complex's database considering biological units(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 49. DOI: 10.2142/Biophys.49.S65_6 |
0.324 |
|
| 2009 |
Jono R, Shimizu K, Terada T. 1P-014 The side chain effects on the conformation of the peptides(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 49. DOI: 10.2142/Biophys.49.S65_5 |
0.31 |
|
| 2009 |
Nakamura S, Kakuta M, Shimizu K. 1P-013 Development of protein local structure prediction method based on combination of multiple support vector machines(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 49. DOI: 10.2142/Biophys.49.S65_4 |
0.349 |
|
| 2009 |
Nishimura A, Terada T, Shimizu K. 3P-041 Multicanonical molecular dynamics simulation of an all-β protein with secondary structure restraints(Protein:Property,The 47th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 49. DOI: 10.2142/Biophys.49.S157_6 |
0.348 |
|
| 2009 |
Furuta T, Shimizu K, Terada T. Accurate prediction of native tertiary structure of protein using molecular dynamics simulation with the aid of the knowledge of secondary structures Chemical Physics Letters. 472: 134-139. DOI: 10.1016/J.Cplett.2009.03.009 |
0.371 |
|
| 2008 |
Terada T, Satoh D, Mikawa T, Ito Y, Shimizu K. Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation. Proteins. 73: 621-31. PMID 18473359 DOI: 10.1002/Prot.22100 |
0.34 |
|
| 2008 |
Morita M, Nakamura S, Shimizu K. Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures. Proteins. 73: 468-79. PMID 18452211 DOI: 10.1002/Prot.22067 |
0.339 |
|
| 2008 |
Kakuta M, Nakamura S, Shimizu K. Prediction of Protein-Protein Interaction Sites Using Only Sequence Information and Using Both Sequence and Structural Information Ipsj Digital Courier. 4: 217-227. DOI: 10.2197/Ipsjdc.4.217 |
0.332 |
|
| 2008 |
Nishimura A, Nishi K, Terada T, Shimizu K. 2P-095 Folding simulation of an all-β protein by molecular dynamics simulation with secondary structure restraints(The 46th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 48. DOI: 10.2142/Biophys.48.S89_6 |
0.334 |
|
| 2008 |
Sumikoshi K, Terada T, Nakamura S, Shimizu K. 2P-027 Protein-protein docking system with refinement stage(The 46th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 48. DOI: 10.2142/Biophys.48.S79_2 |
0.303 |
|
| 2008 |
Kakuta M, Sumikoshi K, Nakamura S, Shimizu K. 3P-290 Prediction of protein-protein interactions using domain sequences(The 46th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 48. DOI: 10.2142/Biophys.48.S172_4 |
0.333 |
|
| 2008 |
Nishi K, Terada T, Shimizu K. 3P-012 Folding simulation of the B-domain of staphylococcal protein A(The 46th Annual Meeting of the Biophysical Society of Japan) Biophysics. 48. DOI: 10.2142/Biophys.48.S129_5 |
0.302 |
|
| 2008 |
Ishitani R, Terada T, Shimizu K. Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations Molecular Simulation. 34: 327-336. DOI: 10.1080/08927020801930539 |
0.369 |
|
| 2008 |
Terada T, Shimizu K. A comparison of generalized Born methods in folding simulations Chemical Physics Letters. 460: 295-299. DOI: 10.1016/J.Cplett.2008.05.066 |
0.327 |
|
| 2007 |
Yamasaki S, Nakamura S, Terada T, Shimizu K. Mechanism of the Difference in the Binding Affinity of E. coli tRNAGln to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop Biophysical Journal. 92: 192-200. PMID 17028132 DOI: 10.1529/Biophysj.106.093351 |
0.335 |
|
| 2007 |
Kakuta M, Sumikoshi K, Nakamura S, Shimizu K. 1P248 Prediction of the residue-based contribution to protein-protein interaction(Bioinformatics-structural, functional, and comparative genomics,Oral Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S85_3 |
0.349 |
|
| 2007 |
Yamasaki S, Nakamura S, Terada T, Shimizu K. 1P132 Dynamical analysis of protein-DNA duplex structures using principal component analysis method(Nucleic acid,Poster Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S56_3 |
0.314 |
|
| 2007 |
Terada T, Shimizu K. 2P106 Comparison of generalized Born models in folding simulations(Proteins-stability, folding, and other physicochemical properties,Oral Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S139_3 |
0.306 |
|
| 2007 |
Nishi K, Terada T, Shimizu K. 2P105 Folding simulation of the B-domain of staphylococcal protein A(Proteins-stability, folding, and other physicochemical properties,Oral Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S139_2 |
0.309 |
|
| 2007 |
Inoue Y, Terada T, Nakamura S, Shimizu K. 2P010 Molecular dynamics simulation of the terminal oxygenase component of carbazole 1,9a-dioxygenase(Proteins-structure and structure-function relationship,Poster Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S115_3 |
0.326 |
|
| 2007 |
Nakamura S, Shimizu K. 2P004 Analysis of sequence-structure relationship of protein loop regions(Proteins-structure and structure-function relationship,Poster Presentations) Seibutsu Butsuri. 47. DOI: 10.2142/Biophys.47.S114_1 |
0.334 |
|
| 2006 |
Ishida T, Nakamura S, Shimizu K. Potential for assessing quality of protein structure based on contact number prediction. Proteins. 64: 940-947. PMID 16788993 DOI: 10.1002/Prot.21047 |
0.351 |
|
| 2006 |
Ishitani R, Shimizu K, Terada T. Evaluation of efficiency of reference potential spatial warping algorithm in conformational sampling of peptides. Journal of Chemical Physics. 124: 214902. PMID 16774437 DOI: 10.1063/1.2200698 |
0.309 |
|
| 2006 |
Satoh D, Shimizu K, Nakamura S, Terada T. Folding free-energy landscape of a 10-residue mini-protein, chignolin. Febs Letters. 580: 3422-3426. PMID 16709409 DOI: 10.1016/J.Febslet.2006.05.015 |
0.358 |
|
| 2006 |
Ishida T, Nakamura S, Shimizu K, Nakai K, Kinoshita K. 2P505 Protein tertiary structure prediction based on contact number prediction(51. New methods and tools (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S422_1 |
0.319 |
|
| 2006 |
Jono R, Terada T, Shimizu K. 2P398 A multicanonical ab initio molecular dynamics method : application to conformation sampling of alanine tripeptide(45. Electronic structure,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S395_2 |
0.305 |
|
| 2006 |
Satoh D, Shimizu K, Nakamura S, Terada T. 1P587 Folding free-energy landscapes of 10-residue proteins(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S293_3 |
0.351 |
|
| 2006 |
Nishi K, Terada T, Shimizu K. 1P573 Folding simulation of the B-domain of staphylococcal protein A(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S290_1 |
0.307 |
|
| 2006 |
Kakuta M, Nakamura S, Shimizu K. 1P486 Prediction of Protein-Protein Interaction Sites Using Evolutionary and Structural Information(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S268_2 |
0.325 |
|
| 2006 |
Nakamura S, Morita M, Kakuta M, Shimizu K. 1P060 Development of a protein tertiary structure prediction server(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S161_4 |
0.34 |
|
| 2006 |
Morita M, Nakamura S, Shimizu K. 1P059 Predicting ligand binding sites of uncharacterized protein structure(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46. DOI: 10.2142/Biophys.46.S161_3 |
0.349 |
|
| 2006 |
Nakamura S, Ishida T, Shimizu K. S2e1-3 Structural propensity of protein fragments and tertiary structure prediction of proteins(S2-e1: "Universality and diversity on the protein-folding problem",Symposia,Abstract,Meeting Program of EABS & BSJ 2006) Biophysics. 46. DOI: 10.2142/Biophys.46.S123_4 |
0.323 |
|
| 2006 |
Jono R, Shimizu K, Terada T. A multicanonical ab initio molecular dynamics method: Application to conformation sampling of alanine tripeptide Chemical Physics Letters. 432: 306-312. DOI: 10.1016/J.Cplett.2006.10.080 |
0.314 |
|
| 2005 |
Ishitani R, Terada T, Nakamura S, Shimizu K. 1P008 Refinement of Comparative-Modeled Protein Structure by Multicanonical Molecular Dynamics Seibutsu Butsuri. 45. DOI: 10.2142/Biophys.45.S33_4 |
0.339 |
|
| 2005 |
Sumikoshi K, Terada T, Nakamura S, Shimizu K. 3P009 Improving the Efficiency of Protein-Protein Docking Prediction by Search Space Reduction Seibutsu Butsuri. 45. DOI: 10.2142/Biophys.45.S206_1 |
0.305 |
|
| 2005 |
Ishida T, Nakamura S, Shimizu K. 2P008 Prediction of protein disordered region from amino acid sequences-Improvement of prediction method with tertiary structure prediction Seibutsu Butsuri. 45. DOI: 10.2142/Biophys.45.S121_4 |
0.316 |
|
| 2005 |
Sumikoshi K, Terada T, Nakamura S, Shimizu K. A fast protein-protein docking algorithm using series expansion in terms of spherical basis functions. Genome Informatics. 16: 161-173. DOI: 10.11234/Gi1990.16.2_161 |
0.322 |
|
| 2004 |
Sumikoshi K, Terada T, Nakamura S, Shimizu K. 2P053 Fast Protein-Protein Docking Prediction Using Series Expansion in terms of Basis Functions Based on Spherical Harmonics Seibutsu Butsuri. 44. DOI: 10.2142/Biophys.44.S123_1 |
0.325 |
|
| 2004 |
Ishitani R, Terada T, Nakamura S, Shimizu K. 2P043 Refinement of Comparative-Modeled Protein Structure by Multicanonical Molecular Dynamics Seibutsu Butsuri. 44. DOI: 10.2142/Biophys.44.S120_3 |
0.339 |
|
| 2004 |
Ishizuka T, Terada T, Nakamura S, Shimizu K. Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson’s equation Chemical Physics Letters. 393: 546-551. DOI: 10.1016/J.Cplett.2004.06.096 |
0.307 |
|
| 2003 |
Nishimura T, Nakamura S, Shimizu K. Application of ab initio prediction of protein structures Seibutsu Butsuri. 43. DOI: 10.2142/Biophys.43.S33_5 |
0.324 |
|
| 2003 |
Ishida T, Nishimura T, Nozaki M, Inoue T, Terada T, Nakamura S, Shimizu K. Development of an ab initio protein structure prediction system ABLE. Genome Informatics. 14: 228-237. DOI: 10.11234/Gi1990.14.228 |
0.352 |
|
| 2002 |
Ishida T, Nakamura S, Shimizu K. 1J1130 Sellecting the best predicted structure in protein tertiary structure prediction Seibutsu Butsuri. 42. DOI: 10.2142/Biophys.42.S55_4 |
0.309 |
|
| 2001 |
Ikeguchi M, Nakamura S, Shimizu K. Molecular dynamics study on hydrophobic effects in aqueous urea solutions. Journal of the American Chemical Society. 123: 677-682. PMID 11456580 DOI: 10.1021/Ja002064F |
0.328 |
|
| 2001 |
Nishimura T, Nakamura S, Shimizu K. Predicting dihedral angles with local sequence similarity in proteins Seibutsu Butsuri. 41. DOI: 10.2142/Biophys.41.S40_4 |
0.307 |
|
| 1999 |
Shimizu S, Ikeguchi M, Nakamura S, Shimizu K. Size dependence of transfer free energies: A hard-sphere-chain- based formalism Journal of Chemical Physics. 110: 2971-2982. DOI: 10.1063/1.477940 |
0.597 |
|
| 1999 |
Shimizu S, Shimizu K. Alcohol Denaturation : Thermodynamic Theory Of Peptide Unit Solvation Journal of the American Chemical Society. 121: 2387-2394. DOI: 10.1021/Ja982560S |
0.573 |
|
| 1999 |
Nakamura S, Hirose H, Ikeguchi M, Shimizu K. Structural modeling of DNA mini-hairpin molecules with various loop sequences Chemical Physics Letters. 308: 267-273. DOI: 10.1016/S0009-2614(99)00574-6 |
0.31 |
|
| 1999 |
Yoshikawa H, Ikeguchi M, Nakamura S, Shimizu K, Doi J. Prediction of protein structure classes and secondary structures by means of hidden Markov models Systems and Computers in Japan. 30: 13-22. DOI: 10.1002/(Sici)1520-684X(19991130)30:13<13::Aid-Scj2>3.0.Co;2-7 |
0.308 |
|
| 1998 |
Sagara J, Shimizu S, Kawabata T, Nakamura S, Ikeguchi M, Shimizu K. The use of sequence comparison to detect ‘identities’ in tRNA genes Nucleic Acids Research. 26: 1974-1979. PMID 9518491 DOI: 10.1093/Nar/26.8.1974 |
0.596 |
|
| 1998 |
and KT, Shimizu K. Molecular Dynamics Simulations in Aqueous Solution: Application to Free Energy Calculation of Oligopeptides Journal of Physical Chemistry B. 102: 6419-6424. DOI: 10.1021/Jp9803788 |
0.314 |
|
| 1998 |
Ikeguchi M, Shimizu S, Nakamura aS, Shimizu K. Roles of Hydrogen Bonding and the Hard Core of Water on Hydrophobic Hydration Journal of Physical Chemistry B. 102: 5891-5898. DOI: 10.1021/Jp980210M |
0.58 |
|
| 1998 |
Ikeguchi M, Shimizu S, Tazaki K, Nakamura S, Shimizu K. Calculation of temperature dependence of free energy caused by potential function changes Chemical Physics Letters. 288: 333-337. DOI: 10.1016/S0009-2614(98)00282-6 |
0.591 |
|
| 1998 |
Shimizu S, Ikeguchi M, Nakamura S, Shimizu K. Molecular Volume, Surface Area, And Curvature Dependence Of The Configurational Entropy Change Upon Solvation : Effects Of Molecular Bonding Chemical Physics Letters. 284: 235-246. DOI: 10.1016/S0009-2614(97)01381-X |
0.579 |
|
| 1998 |
Shimizu S, Ikeguchi M, Shimizu K. An off-lattice theory of solvation: extension of the Flory χ parameter into continuum space Chemical Physics Letters. 282: 79-90. DOI: 10.1016/S0009-2614(97)01147-0 |
0.586 |
|
| 1997 |
Sagara J, Shimizu S, Kawabata T, Nakamura S, Ikeguchi M, Shimizu K. A Novel Method to Detect Identities in tRNA Genes Using Sequence Comparison Genome Informatics. 8: 330-331. DOI: 10.11234/Gi1990.8.330 |
0.58 |
|
| 1997 |
Shimizu S, Ikeguchi M, Shimizu K. Extracting contact free energy from solubility: excluded volume effects of polymers in continuum space Chemical Physics Letters. 268: 93-100. DOI: 10.1016/S0009-2614(97)00165-6 |
0.574 |
|
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