PubRank

Akinori Kidera

Author PubWeight™ 31.49‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Protein structural change upon ligand binding: linear response theory. Phys Rev Lett 2005 1.53
2 Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett 2005 1.16
3 Protonation of the acidic residues in the transmembrane cation-binding sites of the ca(2+) pump. J Am Chem Soc 2005 1.11
4 Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. Proc Natl Acad Sci U S A 2004 1.10
5 Water transport in aquaporins: osmotic permeability matrix analysis of molecular dynamics simulations. Biophys J 2007 1.04
6 Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights. J Chem Phys 2004 0.95
7 Minimum free energy path of ligand-induced transition in adenylate kinase. PLoS Comput Biol 2012 0.95
8 Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors. Acta Crystallogr D Biol Crystallogr 2002 0.95
9 PSCDB: a database for protein structural change upon ligand binding. Nucleic Acids Res 2011 0.94
10 Classification and annotation of the relationship between protein structural change and ligand binding. J Mol Biol 2011 0.94
11 Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. J Mol Biol 2008 0.93
12 Simulation of charge effects on density maps obtained by high-resolution electron crystallography. J Electron Microsc (Tokyo) 2007 0.92
13 Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling. J Am Chem Soc 2012 0.90
14 Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment. Proteins 2008 0.89
15 Ligand mapping on protein surfaces by the 3D-RISM theory: toward computational fragment-based drug design. J Am Chem Soc 2009 0.89
16 Comparative molecular dynamics simulation study of crystal environment effect on protein structure. J Phys Chem B 2012 0.86
17 Ring and zipper formation is the key to understanding the structural variety in all-beta proteins. FEBS Lett 2003 0.81
18 Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. Protein Sci 2009 0.80
19 Side-chain conformational changes of transcription factor PhoB upon DNA binding: a population-shift mechanism. J Am Chem Soc 2010 0.80
20 Linear response theory in dihedral angle space for protein structural change upon ligand binding. J Comput Chem 2009 0.80
21 Comparative simulations of the ground state and the M-intermediate state of the sensory rhodopsin II-transducer complex with a HAMP domain model. Biochemistry 2012 0.80
22 Scalable free energy calculation of proteins via multiscale essential sampling. J Chem Phys 2010 0.80
23 Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Acta Crystallogr D Biol Crystallogr 2007 0.80
24 Functionality mapping on internal surfaces of multidrug transporter AcrB based on molecular theory of solvation: implications for drug efflux pathway. J Phys Chem B 2011 0.79
25 Determination of multicanonical weight based on a stochastic model of sampling dynamics. Phys Rev E Stat Nonlin Soft Matter Phys 2003 0.78
26 Unfolding pathways of goat alpha-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories. J Mol Biol 2007 0.78
27 Multiscale enhanced path sampling based on the Onsager-Machlup action: application to a model polymer. J Chem Phys 2013 0.78
28 Atomically detailed description of the unfolding of alpha-lactalbumin by the combined use of experiments and simulations. J Mol Biol 2005 0.78
29 Probabilistic description of protein alignments for sequences and structures. Proteins 2004 0.78
30 Molecular thermodynamics of trifluoroethanol-induced helix formation: analysis of the solvation structure and free energy by the 3D-RISM theory. Interdiscip Sci 2009 0.77
31 Probabilistic alignment detects remote homology in a pair of protein sequences without homologous sequence information. Proteins 2007 0.77
32 Stochastic formulation of sampling dynamics in generalized ensemble methods. Phys Rev E Stat Nonlin Soft Matter Phys 2004 0.77
33 Solvent friction effects propagate over the entire protein molecule through low-frequency collective modes. J Phys Chem B 2014 0.76
34 SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res 2010 0.76
35 Influence of structural symmetry on protein dynamics. PLoS One 2012 0.76
36 Multivariate frequency domain analysis of protein dynamics. J Chem Phys 2009 0.75
37 Latent dynamics of a protein molecule observed in dihedral angle space. J Chem Phys 2010 0.75
38 Normal mode analysis of protein dynamics in a non-Eckart frame. J Chem Phys 2010 0.75
39 [Conformational changes in proteins are originated from fluctuation: theory of conformational changes in proteins upon ligand binding]. Tanpakushitsu Kakusan Koso 2006 0.75
40 The conserved Arg241-Glu439 salt bridge determines flexibility of the inositol 1,4,5-trisphosphate receptor binding core in the ligand-free state. Proteins 2013 0.75
41 Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways. J Chem Phys 2010 0.75