Haruki Nakamura
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Researcher ORCID ID = 0000-0001-6690-5863
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Computer Science
Haruki Nakamura's Degrees
- PhD Computer Science University of Tokyo
- Masters Computer Science University of Tokyo
- Bachelors Computer Science University of Tokyo
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(Suggest an Edit or Addition)Haruki Nakamura's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Announcing the worldwide Protein Data Bank (2003) (2318)
- The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data (2006) (1013)
- Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009) (568)
- Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices (1994) (477)
- Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive. (2017) (421)
- Protein Data Bank: the single global archive for 3D macromolecular structure data (2018) (347)
- Atomic structure of the RuvC resolvase: A holliday junction-specific endonuclease from E. coli (1994) (282)
- Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks (2006) (268)
- An effective solvation term based on atomic occupancies for use in protein simulations (1993) (263)
- Computer-aided antibody design (2012) (245)
- Structural classification of CDR‐H3 in antibodies (1996) (209)
- Identification of protein biochemical functions by similarity search using the molecular surface database eF‐site (2003) (167)
- PDBML: the representation of archival macromolecular structure data in XML (2005) (164)
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. (2015) (163)
- Silencing the constitutive active transcription factor CREB by the LKB1‐SIK signaling cascade (2006) (161)
- Filtering high-throughput protein-protein interaction data using a combination of genomic features (2005) (159)
- Validation of Structures in the Protein Data Bank (2017) (158)
- H3‐rules: identification of CDR‐H3 structures in antibodies (1999) (154)
- Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers (1992) (154)
- Hub Promiscuity in Protein-Protein Interaction Networks (2010) (151)
- Remediation of the protein data bank archive (2007) (146)
- Community-wide assessment of protein-interface modeling suggests improvements to design methodology. (2011) (139)
- Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format (2011) (132)
- Identification of protein functions from a molecular surface database, eF-site (2004) (131)
- Data Deposition and Annotation at the Worldwide Protein Data Bank (2009) (123)
- Nature of the charge distribution in proteins (1981) (117)
- The Filling Potential Method: A Method for Estimating the Free Energy Surface for Protein−Ligand Docking (2003) (116)
- eF-site and PDBjViewer: database and viewer for protein functional sites (2004) (116)
- BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions (2008) (114)
- Structural classification of CDR‐H3 revisited: A lesson in antibody modeling (2008) (112)
- HitPredict: a database of quality assessed protein–protein interactions in nine species (2010) (111)
- The Protein Data Bank at 40: reflecting on the past to prepare for the future. (2012) (111)
- The Protein Data Bank archive as an open data resource (2014) (109)
- Strong antiferromagnetic spin fluctuations and the quantum spin-liquid state in geometrically frustrated -Mn, and the transition to a spin-glass state caused by non-magnetic impurity (1997) (104)
- OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. (2017) (98)
- A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. (2011) (97)
- Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013) (96)
- Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures (2016) (93)
- Possible mechanisms for the O–O bond formation in oxygen evolution reaction at the CaMn4O5(H2O)4 cluster of PSII refined to 1.9 Å X-ray resolution (2011) (91)
- Identification of the ligand binding sites on the molecular surface of proteins (2005) (91)
- Structure‐based prediction of DNA‐binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces (2004) (91)
- A Novel Approach of Dynamic Cross Correlation Analysis on Molecular Dynamics Simulations and Its Application to Ets1 Dimer–DNA Complex (2014) (88)
- Interaction between the Amino-terminal SH3 Domain of CRK and Its Natural Target Proteins* (1996) (81)
- Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening. (2005) (81)
- Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation (1997) (79)
- Nucleotide Sequence Database Policies (2002) (77)
- The future of the Protein Data Bank. (2013) (75)
- New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj) (2017) (75)
- PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. (2017) (75)
- Protein structure databases with new web services for structural biology and biomedical research (2008) (74)
- Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations (2001) (72)
- Metal Ion Induced Self-Assembly of a Designed Peptide into a Triple-Stranded α-Helical Bundle: A Novel Metal Binding Site in the Hydrophobic Core (1998) (71)
- Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle. (2011) (71)
- PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences (2010) (69)
- Conformational transition states of a β‐hairpin peptide between the ordered and disordered conformations in explicit water (2002) (69)
- Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa values (1992) (68)
- Numerical Calculations of Electrostatic Potentials of Protein-Solvent Systems by the Self Consistent Boundary Method (1987) (66)
- Domain distribution and intrinsic disorder in hubs in the human protein–protein interaction network (2010) (63)
- eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape (2007) (62)
- Two‐component multicanonical Monte Carlo method for effective conformation sampling (1997) (60)
- Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes (2012) (59)
- Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. (2016) (58)
- Labile electronic and spin states of the CaMn4O5 cluster in the PSII system refined to the 1.9 Å X-ray resolution. UB3LYP computational results (2011) (57)
- Protein function annotation from sequence: prediction of residues interacting with RNA (2009) (56)
- Blind prediction of interfacial water positions in CAPRI (2014) (55)
- Protein informatics towards function identification. (2003) (55)
- Molmil: a molecular viewer for the PDB and beyond (2016) (53)
- Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases (2014) (53)
- Systematic classification of CDR‐L3 in antibodies: Implications of the light chain subtypes and the VL–VH interface (2009) (52)
- A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor (2004) (52)
- Non-Ewald methods: theory and applications to molecular systems (2012) (51)
- Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water (2011) (50)
- Application of MDGRAPE‐3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems (2009) (50)
- PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces (2005) (47)
- Comprehensive structural classification of ligand-binding motifs in proteins. (2008) (47)
- Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions. (2013) (46)
- The Worldwide Protein Data Bank (2012) (46)
- High‐resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations (2014) (46)
- Structure and reactivity of the mixed‐valence CaMn4O5(H2O)4 and CaMn4O4(OH)(H2O)4 clusters at oxygen evolution complex of photosystem II. Hybrid DFT (UB3LYP and UBHandHLYP) calculations (2012) (44)
- Kotai Antibody Builder: automated high-resolution structural modeling of antibodies (2014) (44)
- Application of zero-dipole summation method to molecular dynamics simulations of a membrane protein system (2013) (44)
- ASH structure alignment package: Sensitivity and selectivity in domain classification (2007) (43)
- Characteristic spin fluctuations in Y(Mn1-xAlx)2 (1987) (42)
- Visualization of electrostatic recognition by enzymes for their ligands and cofactors (1985) (41)
- Structural basis of the KcsA K(+) channel and agitoxin2 pore-blocking toxin interaction by using the transferred cross-saturation method. (2003) (41)
- Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library (2011) (41)
- Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. (2006) (40)
- Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data (2018) (40)
- Protein‐inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free‐energy barrier distinguishing the native complex from the others (2007) (40)
- Entropic Stabilization of the Tryptophan Synthase α-Subunit from a Hyperthermophile, Pyrococcus furiosus (2001) (39)
- Peptide free‐energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95 (2000) (39)
- Utilization of Methyl Proton Resonances in Cross-Saturation Measurement for Determining the Interfaces of Large Protein–Protein Complexes (2006) (37)
- Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water. (2012) (37)
- Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor. (2017) (37)
- Classification of chemical compounds by protein-compound docking for use in designing a focused library. (2006) (36)
- How community has shaped the Protein Data Bank. (2013) (36)
- Mutational Analysis of Block and Facilitation of HERG Current by A Class III Anti-Arrhythmic Agent, Nifekalant (2007) (34)
- High-frequency dielectric relaxation of water bound to hydrophilic silica gels (1989) (33)
- HINT: a database of annotated protein-protein interactions and their homologs (2005) (33)
- Intramolecular Interaction of SUR2 Subtypes for Intracellular ADP-Induced Differential Control of KATP Channels (2002) (33)
- Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water. (2009) (33)
- 3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity (2014) (33)
- Functional and Structural Analyses of Cryptochrome (2003) (32)
- Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water (2009) (32)
- The multicanonical weighted histogram analysis method for the free-energy landscape along structural transition paths (1999) (31)
- Structure of the entire stalk region of the Dynein motor domain. (2014) (31)
- Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state (2018) (31)
- Energy landscape of a β-hairpin peptide in explicit water studied by multicanonical molecular dynamics (2001) (31)
- The archiving and dissemination of biological structure data. (2016) (30)
- A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent. (2013) (30)
- Tsallis dynamics using the Nosé-Hoover approach. (2002) (30)
- Revisiting antibody modeling assessment for CDR-H3 loop (2016) (29)
- Multiple target screening method for robust and accurate in silico ligand screening. (2006) (28)
- Higher order structure contributes to specific differences in redox potential and electron transfer efficiency of root and leaf ferredoxins. (2006) (28)
- Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold. (2010) (28)
- Two-electron oxidation of water to form hydrogen peroxide sensitized by di(hydroxo)porphyrin GeIV complex under visible-light irradiation (2015) (27)
- Characterization of six mutations in five Spanish patients with mitochondrial acetoacetyl-CoA thiolase deficiency: effects of amino acid substitutions on tertiary structure. (2002) (27)
- Detecting local structural similarity in proteins by maximizing number of equivalent residues (2004) (27)
- Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB (2015) (27)
- Creation of a binuclear purple copper site within a de novo coiled-coil protein. (2012) (27)
- Ab initio MO study of the chlorophyll dimer in the photosynthetic reaction center. I. A theoretical treatment of the electrostatic field created by the surrounding proteins (1997) (27)
- Discrimination between biological interfaces and crystal-packing contacts (2008) (26)
- Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8 (2003) (26)
- In situ extended x-ray absorption fine structure study of initial processes in CdSe nanocrystals formation using a microreactor (2009) (26)
- Similarity search for local protein structures at atomic resolution by exploiting a database management system (2007) (26)
- Virtual‐system‐coupled adaptive umbrella sampling to compute free‐energy landscape for flexible molecular docking (2015) (25)
- Docking of protein molecular surfaces with evolutionary trace analysis (2007) (25)
- Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method. (2011) (25)
- myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme (2016) (24)
- Prediction of protein-ligand complex structure by docking software guided by other complex structures. (2008) (24)
- Consistent Molecular Dynamics Scheme Applying the Wolf Summation for Calculating Electrostatic Interaction of Particles(Atomic and molecular physics) (2008) (24)
- Molecular Dynamics Simulations of Double-Stranded DNA in an Explicit Solvent Model with the Zero-Dipole Summation Method (2013) (24)
- β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain (2003) (24)
- Protein-Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method (2009) (24)
- Electronic and Spin Structures of the CaMn4O5(H2O)4 Cluster in OEC of PSII Refined to 1.9 Å X-ray Resolution (2012) (24)
- In silico prediction of the chemical block of human ether-a-go-go-related gene (hERG) K+ current. (2008) (23)
- Bridging the gap between single-template and fragment based protein structure modeling using Spanner (2011) (23)
- Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida (1992) (23)
- GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures (2005) (23)
- Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. (2010) (23)
- Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling (2016) (22)
- Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes (2011) (22)
- A critical appraisal of the zero-multipole method: Structural, thermodynamic, dielectric, and dynamical properties of a water system. (2016) (22)
- Theoretical investigation of the electronic asymmetry of the special pair cation radical in the photosynthetic type-II reaction center. (2008) (21)
- LigandBox: A database for 3D structures of chemical compounds (2013) (21)
- PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan (2010) (21)
- Model building of a protein-protein complexed structure using saturation transfer and residual dipolar coupling without paired intermolecular NOE (2004) (21)
- Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening (2006) (20)
- Semimetallic behaviour of YInCu4 and LuInCu4 (1994) (20)
- Realism about PDB (2007) (20)
- Time domain measurement of dielectric spectra of aqueous polyelectrolyte solutions at low frequencies (1981) (19)
- Ab initio structural comparison between the tetrahedral intermediates and the phosphorous-containing analogues in the ester and amide hydrolysis (1992) (19)
- Elementary process in polymer chain motion (1982) (18)
- Distinct roles of overlapping and non-overlapping regions of hub protein interfaces in recognition of multiple partners. (2011) (18)
- Multicanonical molecular dynamics algorithm employing an adaptive force-biased iteration scheme. (2004) (18)
- Determination of multicanonical weight based on a stochastic model of sampling dynamics. (2003) (18)
- Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster (2011) (18)
- Molecular dynamics study on mobility and dipole ordering of solvent around proteins: effects of periodic-box size and protein charge (1999) (18)
- Density functional study of roles of porphyrin ring in electronic structures of heme (2009) (18)
- Electronic structures of a [4Fe–4S] cluster, [Fe4S4(SCH3)3(CH3COO)], in dark-operative protochlorophyllide oxidoreductase (DPOR) (2011) (17)
- A new approach to illustrating electrostatic molecular surfaces (1984) (17)
- In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design (2009) (17)
- Nuclear magnetic resonance study of magnetic correlation in the heavy-fermion superconductor CeCu2Si2 (1992) (17)
- Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics (2012) (16)
- The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems. (2014) (16)
- Nature of the Charge Distribution in Proteins. III. Electric Multipole Structures (1985) (16)
- Density functional study of molecular interactions in secondary structures of proteins (2016) (16)
- Construction of an extended invariant for an arbitrary ordinary differential equation with its development in a numerical integration algorithm. (2006) (16)
- Ab initio study of magnetic interactions of manganese-oxide clusters (2011) (16)
- An Efficient in Silico Screening Method Based on the Protein-Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands (2006) (15)
- Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95 (2000) (15)
- The effect of the side chain length of Asp and Glu on coordination structure of Cu(2+) in a de novo designed protein. (2009) (15)
- Numerical Calculations of Reaction Fields of Protein-Solvent Systems (1988) (15)
- Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations (2016) (15)
- Quantitative Structure‐activity Relationship (QSAR) Models for Docking Score Correction (2016) (15)
- Precise and Easy Method of TDR to Obtain Dielectric Relaxation Spectra in GHz Region (1982) (15)
- Computational Study of Drug Binding Affinity to Influenza A Neuraminidase Using Smooth Reaction Path Generation (SRPG) Method (2015) (15)
- Application of Time Domain Reflectometry Covering a Wide Frequency Range to the Dielectric Study of Polymer Solutions (1982) (14)
- Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase (2006) (14)
- β-hairpin folds by molecular dynamics simulations (2000) (14)
- Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation (2016) (14)
- Generalized simulated tempering realized on expanded ensembles of non-Boltzmann weights. (2004) (14)
- Physicochemical evaluation of protein folds predicted by threading (2000) (14)
- Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of structural asymmetry and protein environment (2007) (14)
- Nuclear magnetic resonance in the antiferromagnetic heavy-fermion system UCu5: spin reorientation at 1 K (1994) (14)
- Density functional study of porphyrin distortion effects on redox potential of heme (2018) (13)
- Theoretical studies of the magnetic couplings and the chemical indices of the biomimetic models of oxyhemocyanin and oxytyrosinase (2009) (13)
- Site-directed removal of N-glycosylation sites in BST-1/CD157: Effects on molecular and functional heterogeneity (2001) (13)
- Protein-ligand docking guided by ligand pharmacophore-mapping experiment by NMR. (2011) (13)
- An Application of Fourier Synthesis to Pseudorandom Noise Dielectric Spectrometer (1977) (13)
- Evaluation of the conformational equilibrium of reduced hen egg lysozyme by antibodies to the native form. (2010) (13)
- A method of comparing protein molecular surface based on normal vectors with attributes and its application to function identification (2002) (13)
- Magnetic and transport properties in the low-carrier system Gd1-xLuxInCu4 (1994) (13)
- Structural genomics of membrane proteins. (2003) (12)
- Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling (2016) (12)
- PreBI: prediction of biological interfaces of proteins in crystals (2006) (12)
- Efficiency in the Generation of the Boltzmann−Gibbs Distribution by the Tsallis Dynamics Reweighting Method (2004) (12)
- A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening (2008) (12)
- Membrane attachment facilitates ligand access to the active site in monoamine oxidase A. (2009) (12)
- Weak points of antiparallel β-sheets. How are they filled up in globular proteins? (1993) (12)
- Multidimensional virtual‐system coupled canonical molecular dynamics to compute free‐energy landscapes of peptide multimer assembly (2019) (12)
- Model Building of Antibody-Antigen Complex Structures Using GBSA Scores (2016) (12)
- Continuum Mechanical Parameterisation of Cytoplasmic Dynein from Atomistic Simulation. (2020) (12)
- Enhancement of canonical sampling by virtual-state transitions. (2017) (12)
- SeSAW: balancing sequence and structural information in protein functional mapping (2010) (11)
- Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent (2007) (11)
- Functional annotation by sequence‐weighted structure alignments: Statistical analysis and case studies from the Protein 3000 structural genomics project in Japan (2008) (11)
- Safeguarding the integrity of protein archive (2010) (11)
- Dielectric measurements of solutions of poly-γ-benzyl-L-glutamate using a pseudo-random noise dielectric spectrometer (1977) (11)
- A challenge towards next-generation research infrastructure for advanced life science (2009) (11)
- Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder. (2019) (11)
- Orientation of Sperm DNA under a Magnetic Field (1995) (11)
- Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation (2004) (11)
- Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins (2011) (11)
- How A Novel Scientific Concept Was Coined the “Molten Globule State” (2020) (11)
- Editorial for the Special Issue of Biophysical Reviews focused on the Biophysical Society of Japan with select scientific content from the 57th BSJ annual meeting, Miyazaki, Japan (2020) (11)
- Molecular mechanisms of cooperative binding of transcription factors Runx1–CBFβ–Ets1 on the TCRα gene enhancer (2017) (11)
- Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations (2009) (10)
- Prediction of Protein−compound Binding Energies from Known Activity Data: Docking‐score‐based Method and its Applications (2018) (10)
- Integration of Ligand-Based Drug Screening with Structure-Based Drug Screening by Combining Maximum Volume Overlapping Score with Ligand Doscking (2012) (10)
- Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism (2019) (10)
- Calculation of protein-ligand binding free energy using smooth reaction path generation (SRPG) method: a comparison of the explicit water model, gb/sa model and docking score function. (2009) (10)
- Dynamical origin of uniform sampling in multicanonical ensemble. (2003) (10)
- Calibration of force‐field dependency in free energy landscapes of peptide conformations by quantum chemical calculations (2002) (10)
- A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening (2006) (10)
- Nature of Protein Family Signatures: Insights from Singular Value Analysis of Position-Specific Scoring Matrices (2007) (10)
- Multi-dimensional virtual system introduced to enhance canonical sampling. (2017) (9)
- Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs) (2010) (9)
- Average energy guided simulated tempering implemented into molecular dynamics algorithm for protein folding simulation (2004) (9)
- Molecular dynamics simulation study on water associated with π-electrons of benzene by using QM/MM potential (2006) (9)
- Pretransitional Phenomena in the Isotropic Phase of a Lyotropic Liquid Crystal of Bacterial Virus fd. (1983) (9)
- Does B3LYP correctly describe magnetism of manganese complexes with various oxidation numbers and various structural motifs (2012) (9)
- Resonating broken symmetry CI approach for ion-radical systems: Comparison with UHF, hybrid-DFT, and CASSCF-DFT (2008) (9)
- Electronic structures of heme a of cytochrome c oxidase in the redox states—Charge density migration to the propionate groups of heme a (2009) (9)
- A new method for in-silico drug screening and similarity search using molecular dynamics maximum volume overlap (MD-MVO) method. (2009) (9)
- Protein-protein interactions on the surface of immunoglobulin molecules (1989) (9)
- Collective motions of myosin head derived from backbone molecular dynamics and combination with X‐ray solution scattering data (2001) (9)
- Data deposition and annotation at the worldwide protein data bank. (2008) (9)
- Dynamical origin of enhanced conformational searches of Tsallis statistics sampling. (2004) (9)
- Multicanonical molecular dynamics simulations combined with Metadynamics for the free energy landscape of a biomolecular system with high energy barriers (2011) (9)
- Dielectric studies of aqueous solutions of poly(L‐glutamic acid) (1981) (9)
- Virtual states introduced for overcoming entropic barriers in conformational space (2012) (9)
- Mutational and Structural Analyses of Caldanaerobius polysaccharolyticus Man5B Reveal Novel Active Site Residues for Family 5 Glycoside Hydrolases (2013) (9)
- Nature of the Charge Destribution in Proteins. II. Effect of Atomic Partial Charges on Ionic Charges (1985) (9)
- Improved Estimation of Protein-Ligand Binding Free Energy by Using the Ligand-Entropy and Mobility of Water Molecules (2013) (9)
- Electrostatic Complementarities between Guest Ligands and Host Enzymes (1985) (8)
- Flexible docking of an amyloid‐forming peptide from β2‐microglobulin (2006) (8)
- Structure determination of a protein assembly by amino acid selective cross‐saturation (2011) (8)
- Parallelization of Markov Chain Generation and its Application to the Multicanonical Method (2008) (8)
- Definition of Drug-Likeness for Compound Affinity (2011) (8)
- Resonating coupled-cluster CI approach to ion-radical systems: Comparison with the unrestricted coupled-cluster approach (2009) (8)
- Linear response function approach for the boundary problem of QM/MM methods (2013) (7)
- Electronic structures of the Cu2S2 core of the CuA site in cytochrome c oxidase and nitrous oxide reductase (2012) (7)
- Anomalous Hydrodynamic Behavior of Smectic Liquid Crystals at Low Frequencies (1987) (7)
- Solvent flow patterns fluctuating largely around a protein and correlation with solvent density fluctuations: A molecular dynamics study. (2010) (7)
- Identification of diphtheria toxin R domain mutants with enhanced inhibitory activity against HB-EGF. (2015) (7)
- Design and synthesis of an α‐helical peptide containing periodic proline residues (1992) (7)
- Stochastic formulation of sampling dynamics in generalized ensemble methods. (2004) (7)
- Hydrogen bond donors and acceptors are generally depolarized in α‐helices as revealed by a molecular tailoring approach (2019) (7)
- Ab initioMO calculations of the chlorophyll dimer in the photosynthetic reaction center (1990) (7)
- The dominance model for heterosis explains culm length genetics in a hybrid sorghum variety (2021) (7)
- Advanced in-silico drug screening to achieve high hit ratio (2009) (7)
- Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation. (2011) (7)
- Psychological Impact of COVID-19 on Occupational Therapists: An Online Survey in Japan. (2021) (6)
- Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70th birthday (2018) (6)
- Observation of the side-chain motion of polypeptides in solution by measurement of picosecond dielectric relaxation (1981) (6)
- Finding ligands for G protein-coupled receptors based on the protein-compound affinity matrix. (2007) (6)
- Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening. (2006) (6)
- Deterministic generation of the Boltzmann–Gibbs distribution and the free energy calculation from the Tsallis distribution (2003) (6)
- Counterbalance of ligand‐ and self‐coupled motions characterizes multispecificity of ubiquitin (2013) (6)
- Theoretical Investigation on Nearsightedness of Finite Model and Molecular Systems Based on Linear Response Function Analysis (2014) (6)
- Exhaustive comparison and classification of ligand-binding surfaces in proteins (2013) (6)
- Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities (2021) (6)
- SUBSECOND MEASUREMENT OF DIELECTRIC DISPERSION (1977) (6)
- Reply to: Building meaningful models of glycoproteins (2007) (6)
- Magnetostriction of ytterbium-based Kondo compounds YbXCu4 (X = In, Ag and Au) (1999) (6)
- Modelling of third cytoplasmic loop of bovine rhodopsin by multicanonical molecular dynamics. (2004) (6)
- The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks (2007) (6)
- Big data science at AMED-BINDS (2020) (6)
- Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins (2016) (6)
- Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase: the origin of stronger antiferromagnetic couplings than other purple acid phosphatases. (2009) (6)
- Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling. (2020) (6)
- Correction: Patil, A. et al. Hub Promiscuity in Protein-Protein Interaction Networks. Int. J. Mol. Sci. 2010, 11, 1930-1943 (2010) (6)
- Editors’ Roundup: June 2022 (2022) (5)
- Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation (2012) (5)
- Enhanced free-energy calculation using multiscale simulation. (2010) (5)
- Structure and Function of Macrophage Scavenger Receptors (1994) (5)
- Threshold electric fields controlled by surface treatments in KTaO3 field-effect transistors (2010) (5)
- Locality and nonlocality of electronic structures of molecular systems: Toward QM/MM and QM/QM approaches (2012) (5)
- Molecular dynamics coupled with a virtual system for effective conformational sampling (2018) (5)
- Rigid‐body motions of interacting proteins dominate multispecific binding of ubiquitin in a shape‐dependent manner (2014) (5)
- Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding (2006) (5)
- CryoEM Models and Associated Data Submitted to the 2015/2016 EMDataBank Model Challenge (2018) (4)
- Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling (2020) (4)
- The Protein Data Bank (PDB) and the Worldwide PDB http://www.wwpdb.org (2005) (4)
- PDB 40 : The Protein Data Bank Celebrates its 40 th Birthday (4)
- Comment on On the propagation of errors by Jaskolski (2013) (2013) (4)
- An Efficient in Silico Screening Method Based on the Protein—Compound Affinity Matrix and Its Application to the Design of a Focused Library for Cytochrome P450 (CYP) Ligands. (2007) (4)
- Molecular dynamics sampling scheme realizing multiple distributions. (2005) (4)
- Apparatus for Measurement of Complex Shear Modulus of Liquid Crystals at Low Frequencies (1987) (4)
- Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions (2016) (4)
- myPresto/omegagene 2020: a molecular dynamics simulation engine for virtual-system coupled sampling (2020) (4)
- GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution (2012) (4)
- A Theoretical Approach to a Novel Pathway of Proton Translocation of Cytochrome c Oxidase (2008) (4)
- Berman, Henrick, Nakamura & Arnold respond [2] (2006) (3)
- Density functional study of the phosphate diester hydrolysis of RNA in RNA/DNA hybrid by RNase HI (2014) (3)
- CAD–ICAD complex structure derived from saturation transfer experiment and simulated annealing without using pairwise NOE information (2004) (3)
- A resonating broken-symmetry CI study of cationic states of phenalenyl dimeric compounds (2009) (3)
- Development of PDBj-ML (2002) (3)
- Protein informatics towards integration of data grid and computing grid (2005) (3)
- A general ab initio approach for free energy landscapes of biological molecules around the transition states (1999) (3)
- Linear response function of the Mayer bond order: an indicator to describe intrinsic chemical reactivity of molecules (2015) (3)
- Quantum chemical studies on hydrogen bonds in helical secondary structures (2022) (3)
- Improvement of Protein-Compound Docking Scores by Using Amino-Acid Sequence Similarities of Proteins (2008) (3)
- A Similarity Search Using Molecular Topological Graphs (2009) (3)
- Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis–trans isomerization of N-Methylacetamide (2011) (3)
- Theoretical Investigation of the Electronic Asymmetry of the Special Pair Cation Radical in the Photosynthetic Type-II Reaction Center (2008) (2)
- Dielectric behavior of 2-methyl-2-propanol and butanol isomers in solutions (1985) (2)
- Hydrogen Bond Donors and Acceptors are Generally Depolarized in α-Helices as Revealed by a Molecular Tailoring Approach (2019) (2)
- Some reflections on a career in science and a note of thanks to the contributors of this Special Issue (2022) (2)
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference (2022) (2)
- Structure-based functional annotation of protein sequences guided by comparative models (2008) (2)
- Flexible docking of an amyloid-forming peptide from beta(2)-microglobulin. (2006) (2)
- Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction (2009) (2)
- Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists (2013) (2)
- Geometric and electrochemical properties of complexes consisting of two aminonaphthoquinone-bound Schiff-base ligands and MnII, FeII, NiII, CuII, or ZnII (2015) (2)
- Dielectric studies on synthetic and natural polyelectrolytes (1988) (2)
- Coordination effects on the electronic structure of the CuA site of cytochrome c oxidase (2012) (2)
- Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics (2014) (2)
- Extraction of recombinant protein from Escherichia coli by using a novel cell autolysis activity of VanX. (2013) (2)
- mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories (2016) (2)
- Integrative Structural Biology with Hybrid Methods (2018) (2)
- Ultrasonic Resonance Spectrometry with Fourier Synthesized Pseudorandom Noise Excitation and Its Application to a Lyotropiec Liquid Crystal (1982) (2)
- Structure of a DNA octamer, d(CCTTAAGG)2 obtained by restrained molecular dynamics based on Raman and NMR data (1991) (2)
- Instability In Chemical Bonds: Uno Cascc, Resonating Ucc And Approximately Projected Ucc Methods To Quasi-Degenerate Electronic Systems (2010) (2)
- Announcing changes to the publishing procedures of “Biophysics and Physicobiology” (BPPB)—the Biophysical Society of Japan’s English language biophysics journal (2021) (2)
- Nearsightedness-related indices of finite systems based on linear response function: one-dimensional cases (2015) (2)
- Deterministic design for Tsallis distribution sampling (2005) (2)
- Faster Binding Free-Energy Landscape Calculation by Virtual-State Coupled Adaptive Umbrella Sampling (2016) (2)
- Electron density based interaction energy estimation of the special pair in the photosynthetic reaction center (2012) (2)
- Different Impacts of COVID-19 on Quality of Therapy, Psychological Condition, and Work Life Among Occupational Therapists in Physical and Mental Health Fields (2022) (2)
- Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction (2010) (2)
- Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities (2009) (2)
- Side-chain Conformations Cooperatively Restricted in Protein Secondary Structure. II. Side-chain Configurational Entropies of .ALPHA.-helices in the Folding Nuclei. (1996) (2)
- Orbital ordering in BaVS3 (1999) (2)
- Analysis of Complementarity of Protein-DNA Interactions Using the Electrostatic Potential and the Molecular Surface Geometry (2002) (2)
- Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013) (2013) (1)
- The Multicanonical Weighted Histogram Analysis Method for the Free Energy Landscape along Structural Transition Paths (2000) (1)
- Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures. (2013) (1)
- Cu nuclear magnetic resonance study of the magnetic structure in NdCu2 (1995) (1)
- New Features of PDBj-ML, an XML Format for Protein Data Bank (2002) (1)
- A case of Leydig cell tumor of the testis in a patient with Klinefelter's syndrome. (1987) (1)
- COMPUTER AIDED DESIGN OF ARTIFICIAL PROTEINS (1991) (1)
- Theoretical studies of electrostatic effect of protein environment on electronic structures and chemical indices of the active site of oxygenated and deoxygenated hemerythrin (2013) (1)
- Model Building Study of Complex Structures Using NMR Chemical Shift Change Information (1997) (1)
- Spin reorientation driven by energy gap formation in UCu5 (1995) (1)
- Multiangular method for analysing molecular geometry from nuclear overhauser effect results (1986) (1)
- A study of the heating effect on mouse liver after Cryosurgery (2007) (1)
- Ab initio DFT study of magneto-structural correlation of dinuclear mixed-valence Mn complexes (2013) (1)
- Molecular Dynamics Simulations of Dynein Motor Domain in Explicit Water (2014) (1)
- In-silico drug screening method based on the protein-compound affinity matrix using the factor selection technique. (2007) (1)
- Comparison of Geometries and Properties of Protein Molecular Surface for Structure-Based Function Prediction (2000) (1)
- The Structural Origin of the Electronic Asymmetry of the Special Pair in the Photosynthetic Reaction Center: Quantum Chemical and Bioinformatics Approaches (2009) (1)
- S08I2 Functional Annotation Sequence-weighted Structure Alignments(Bioinformatics in the Era of Structural Proteomics) (2007) (1)
- Dielectric Relaxation Measurements of Hydrated Powder at Subzero Temperatures by Time-Domain Reflectometry (1988) (1)
- How to determine boundaries for QM/MM calculations: A guideline based on linear response function for glutathione (2013) (1)
- Non-Ewald methods: theory and applications to molecular systems (2012) (1)
- Nuclear magnetic relaxation in the ordered state of UCu5 (1996) (1)
- Reply to: Is one solution good enough? (2006) (1)
- Response to On prompt update of literature references in the Protein Data Bank (2014) (1)
- Theoretical studies on electronic structure and magnetic properties of mixed-valence uteroferrin active site (2011) (1)
- Protein Data Bank Japan (PDBj): an interview with Haruki Nakamura of Osaka University by Wendy A. Warr. (2011) (1)
- Announcement of BPPB paper awards 2022 (2022) (0)
- Formation of betha-hairpin by molecular dynamics simulations (2000) (0)
- 1PT168 Effect of flexibility and electrostatic interaction on rapid binding and unbinding of an intrinsically disordered protein(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- Elastic Property of Dynein Motor Domain Obtained from All-Atom Molecular Dynamics Simulations in Explicit Water (2015) (0)
- 2P-044 Structural diversity of hetero-dimers : insights from the study of predicting protein-protein complex structures(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Development of structural biology. What and how far is proven ? 4. Computer science in structural biology. (1999) (0)
- Drug Development Value Chain Constructed by Collaboration Between The SOSHO Project and The NPO BIOGRID (2007) (0)
- Data Deposition Supporting Website at Osaka for BioMagResBank and Protein Data Bank (2008) (0)
- 3P-260 Theoretical study on the interaction of the special pair in the photosynthetic reaction center(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 1P-007 Multicanonical molecular dynamics simulation of a protein with 57 residues in explicit water(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 1P047 QM/MM simulation study on the mechanism of cis-trans isomerization of human Pin1 protein(Proteins-functions,Poster Presentations) (2007) (0)
- 1I1645 Nonglassy downhill folding in a 3D lattice Go model protein (2002) (0)
- 3P-224 Theoretical analysis of the side group rotamers of chlorophyll(Photobiology:Photosynthesis,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- Density functional studies of the structural variety of the Cu2S2 core of the CuA site (2012) (0)
- NMR Measurements on Cerium and Uranium Compounds (1994) (0)
- Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease ( 1 DIFA ) by a coarse-grained Monte Carlo simulation (2015) (0)
- 2P-049 Computational approach to the coupled folding and binding in the interaction between pKID and the KIX domain(Protein:Property,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- 3P294 Structural modeling for protein complexes using small angle x-ray scattering(Bioinformatics: Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- S3c2-1 Protein Function Analyses from Structural Bioinformatics Approach(S3-c2: "Structural Bioinformatics: Molecular structures as the basis of understanding protein network systems",Symposia,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 3PT010 Molecular Dynamics Simulations of Ets1-DNA complexes using Zero-Dipole Summation Method(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- Coupled Folding and Binding of pKID with KIX Domain Investigated by Multicanonical Molecular Dynamics Simulation in Explicit Solvent (2010) (0)
- Using Sequence Homology to Filter High-throughput Protein-protein Interaction Data (2004) (0)
- 1E1700 Fast 2D chemical search based on maximum common substructure and molecular descriptors(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 1J1345 Folding simulations of a beta-hairpin peptide (2002) (0)
- Chemical Indices of the Biomimetic Models of Oxyhemocyanin and Oxytyrosinase (2011) (0)
- A Comparison of 3D Conformations of Endothelin-1 Analogs to Find the Pharmacophore Model Required for Endothelin Receptor Ligand Activity (2014) (0)
- Problemes associated with electrostatic field of proteins. (1989) (0)
- In silico approaches to drug repositioning for COVID-19 at AMED-BINDS (2020) (0)
- 1P138 1YA0945 Electronic structures of the novel [4Fe-4S] cluster in dark-operative protochlorophyllide oxidoreductase(Electronic state,Early Research in Biophysics Award Candidate Presentations,Early Research in Biophysics Award,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- A QM/MM Molecular Dynamics Simulation Study of the Cis-Trans Isomerization Process of N-Methylacetamide (2011) (0)
- Searching and viewing hybrid structure data (2017) (0)
- A new local drug delivery system for the uterus using bio-nanocapsule (BNC) (2014) (0)
- Composite structural motifs of interaction interfaces for delineating biological functions of proteins (2011) (0)
- 3G1024 Ligand-dependent conformational changes of the promiscuous protein : A case for Ubiquitin(3G Protein: Structure 3,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Evolvement to hepatitis B virus carrier after co-infection with cytomegalovirus-a case report. (1999) (0)
- Play with three-dimensional structure data of biomolecules – PDBj (2017) (0)
- Improve publishing procedures of Biophysics and Physicobiology (2021) (0)
- 2B1436 A multi-body potential for normal mode analysis of protein structure(Proteins:Structure & Function II:Theory, Aggregation,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 1P098 Computational study of the electronic structures of hemes in cytochrome c_3(02. Heme proteins,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Kinetic characterization of a DNA binding activity of the transcription factor Ets1 and its regulation by phosphorylation in an intrinsically disordered region (2016) (0)
- Structural alterations in the cytoplasmic region of G protein-gated inward rectifier potassium channel, Kir3.2 (2009) (0)
- 3PT190 Ensemble Docking Simulation for fa Adrenergic Receptor Using Elastic Network Models(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 3P003 Segmentation & fitting algorithm for multiple subunit fitting into a low resolution density map(01A. Protein: Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Folding/unfolding molecular dynamics simulations of a beta-hairpin peptide (2001) (0)
- 1J1400 Folding and unfolding mechanisms of helical peptide through free energy landscape (2002) (0)
- 1P049 Free-energy landscape of the C-terminal negative regulatory domain of p53(01C. Protein : Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Data quality in the PDB archive (2008) (0)
- 3P-270 The acceptation of NMR data deposition for biological small molecule structure (SMSDep) have been started at BMRB in Japan(Miscellaneous topics,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- Relationship between sequence and structure of CDR-H3 in antibodies (2008) (0)
- A Method of Protein Molecular Surface Comparison Based on Geometric Hashing (2000) (0)
- 3P-034 Hybrid DFT study on the electronic structure of active site of pweet potato purple acid phosphatase(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Molecular behavior of a higher-order complex of multiple transcription factors on enhancer site upon phosphorylation (2016) (0)
- Overall Introduction and Rationale, with View from Computational Biology. (2018) (0)
- Homcos : A Server to Search and Model 3D Structures of Protein-Protein and Compound-Protein Complexes (2014) (0)
- Development of the Method of the Calculation for Hybrid QM/MM Simulation (2003) (0)
- Promotion of Biophysics and Physicobiology (2020) (0)
- Issue Information (2017) (0)
- Understanding folding/unfolding mechanisms of a beta-hairpin peptide through energy landscape (2001) (0)
- An Enhanced Conformational Sampling of a 40-Residue Protein Consisting of Alpha and Beta Secondary Structures in Explicit Solvent (2008) (0)
- 3P001 The Changes of Database Enrichment for in silico screening by using modeling proteins (2005) (0)
- 3P-117 Fair current, vortex, and drying/wetting water flow around lysozyme investigated by molecular dynamics simulation(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Zero-Dipole Summation Method for Precisely Estimating Electrostatic Interactions in Molecular Simulation (2012) (0)
- 1G1548 Evaluation and improvement of low-resolution structure comparison system for extensive 3D electron microscopy data(Protein: Structure 1,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 2P455 Web service of the Protein Data Bank Japan (PDBj)(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 3P293 High-throughput and Low-resolution structure comaprison of 3D electron microsocpy data(Bioinformatics: Structural genomics,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- Theoretical Study of Magnetism of Manganese Clusters (2014) (0)
- Ag eneral ah initio approach for free energy landscapes of biological molecules around the transition states Fusion of the classical molecular mechanics simulation and the quantum chemical calculation (2006) (0)
- 2P098 Development of the Method of Hybrid QM/MM Simulation including chemical bond on QM/MM boundary (2005) (0)
- 2P-283 PiRaNhA: prediction of RNA-binding residues from protein sequence(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Crystal Structure of a glycoside hydrolase (2013) (0)
- 3P014 Theoreical analysis of molecular interactions in secondary strucutures of proteins(01A. Protein: Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1P-074 Sampling enhancement for all-atom simulation using coarse-grained model(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 2D1436 Characteristic electronic structures of a novel [4Fe-4S] cluster in dark-operative protochlorophyllide oxidoreductase(DPOR)(Protein: Structure & Function 1,The 48th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 2P354 Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center : Effect of protein environment(43. Photosynthesis,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- Parameter Identification of Elastic Modulus of Rock Based on Blast Vibration by Adjoint Equation Method (0)
- Molecular mechanism for modulation of a multiple transcription factor complex formed on enhancer site upon phosphorylation (2016) (0)
- Issue Information (2019) (0)
- Proteomics Research at the Institute for Protein Research, Osaka University (2007) (0)
- 1P118 A Computational Study of Monoamine Oxidase A Dynamics(Membrane proteins,Poster Presentations) (2007) (0)
- The wwPDB and future perspectives in sharing macromolecular data (2011) (0)
- 3P008 Using 3D electron microscopy data by EM Navigator and Yorodumi(01A. Protein: Structure,Poster) (2013) (0)
- 3P-038 Ab Initio QM/MM simulation studies on the cis-trans Isomerization of Human Pin 1 Enzyme(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Archiving activities of the Protein Data Bank at Osaka university (2002) (0)
- 1P482 Structural based analysis of protein-sugar binding sites(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 1P-081 Density Functional Study of Roles of Porphyrin Ring in Electronic Structures of Heme(Heme proteins, The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- 1P045 Molecular simulations of protein-ligand structures constructed by computational docking(Proteins-functions,Poster Presentations) (2007) (0)
- CDR-H3 Conformation Determining the Maturation Pathway of an Antibody (2000) (0)
- OneDep: wwPDB system for deposition, biocuration, validation of macromolecular structures (2017) (0)
- Information Extraction from Semi-Structured Data in the Protein Data Bank by Induction of a Data Description Pattern (2003) (0)
- 1P264 Molecular dynamics study on cooperative binding of Ets1 and partner transcription factors on regulatory elements(22A. Bioinformatics:Structural genomics,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 3PT223 Computational study of the phosphodiester hydrolysis of RNA by RNase H(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 1P004 Brownian dynamics simulation on HERG ion-channel permeation (2005) (0)
- 2P580 Susceptibility of the hit ratio at in-silico drug screening to protein structures(55. Drug design and delivery,Poster Session,Abstract,Meeting Program of EABS &BSJ 2006) (2006) (0)
- A filtering method for high-speed retrieval of similar active sites (2002) (0)
- Parameter Identification of Elastic Modulus at Futatsuishi Site (2006) (0)
- 1P270 New classification of the structures of antibody CDR-H3(Genome,Poster Presentations) (2007) (0)
- 2P308 Simple and easy application of Wang-Landau method to molecular dynamics simulations(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 1P155 Elastic property of dynein motor domain obtained from all-atom molecular dynamic simulations in explicit water(11. Molecular motor,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 29pPSA-42 ^ Si-NMR study of URu_2Si_2 under pressure (2006) (0)
- Design strategy for protein stability: stable local conformation in consistency with the global conformation (1993) (0)
- Structural analysis of anti-NP antibody, B2, in vacuo and water (2000) (0)
- EM Navigator – 3D electron microscopy data navigator (2008) (0)
- De novo design and creation of artificial proteins (1993) (0)
- Analysis of Complementarity of Protein-Protein and Protein-DNA Interactions Using the Molecular Surface Database, eF-site (2001) (0)
- 1P292 Structural based analysis and classification of protein-carbohydrate interactions (2005) (0)
- 3G1358 Flexible docking between antigen and antibody by multicanonical molecular dynamics simulation(3G Protein: Structure 4,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- Small-molecule ligand/drug representation and validation in the Protein Data Bank (2017) (0)
- The Papers that Influenced My Career: Creamer and Rose (2020) (0)
- 2P-282 Antibody canonical structures for CDR-L3 revisited(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- 3P004 Shape comparison of 3D electron microscopy data using both feature-vectors and GMM-based superimpositions(01A. Protein: Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- 1P015 Quantum chemical study of intra- and inter-molecular interactions in secondary structures(01A. Protein:Structure,Poster) (2013) (0)
- Nuclear magnetic relaxation in CeCu2 (1996) (0)
- Improvement of Protein‐Compound Docking Scores by Using Amino‐Acid Sequence Similarities of Proteins. (2008) (0)
- 1PT119 Similarity search system for low-resolutin 3D-EM strcutre data in EM Data Bank and Protein Data Bank(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 3P116 Structural Fundamentals for Monoamine Oxidase A Inhibition Control Revealed by Molecular Dynamics Simulations (2005) (0)
- Development of a Scoring Method for Predicting Protein Complex Structures (2008) (0)
- 3D1036 P17 Composite structural motifs of interaction interfaces for delineating biological functions of proteins(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- RIBONUCLEASE H: FULL ASSIGNMENT OF BACKBONE PROTON RESONANCES WITH HETERONUCLEAR 3D NMR AND SOLUTION STRUCTURE (1991) (0)
- 2P011 EM Navigator-Electron microscopy data browser(Proteins-structure and structure-function relationship,Poster Presentations) (2007) (0)
- 1P016 Superimposing density maps and atomic models of macromolecular complexes using Gaussian mixture model(01A. Protein:Structure,Poster) (2013) (0)
- 2SP6-01 Introduction : From atomic structures to electronic structures of biological macromolecules(2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- 2P084 Study on 4'-Phosphopantetheinyl Transfer Reactions to Acyl Carrier Protein : the preliminary processes of Human Fatty Acid Synthesis(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- Proceedings of the 26th annual meeting Chiba, Japan, October 18–20, 1984 (1985) (0)
- 3P277 A theoretical study of the primary charge-separation process in the photosynthetic reaction center (2005) (0)
- 1P-104 Ab initio QM/MM study of photosynthesis reaction center of Rhodobacter sphaeroides(Electronic state, The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- 3H0936 Free-energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein by all-atom simulations(3H Protein: Property 4,The 49th Annual Meeting of the Biophysical Society of Japan) (2011) (0)
- 2P-039 Sampling enhancement for all-atom simulation using coarsegrained model(Protein:Property,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- 2PT103 3D complex structure assignment for evolutionary conserved protein-protein interactions(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- A spin density version of linear response function: Toward guidelines of QM/MM boundaries for reliable computations (2014) (0)
- A case of porphyria cutanea tarda which was improved by phlebotomy. (1986) (0)
- Side-chain Conformations Cooperatively in Protein Secondary Structure I. A Novel Method for Exhaustive Structure Restricted Searching (2006) (0)
- H3-Rules, Progress Report 2007 (2008) (0)
- 1PT126 Atoms in molecules analysis of hydrogen-bond interactions in α- helix, and β-sheets of protein(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 3P036 Molecular dynamics simulaion of prion using Janus-type Go model (2005) (0)
- 1P048 Flexible docking multicanonical molecular dynamics simulations between factor Xa and its inhibitors(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- Smoothed Wang-Landau Sampling of a Peptide in Aqueous Solution (2011) (0)
- Multi-level/Multi-scale Simulations towards Physiome Research (2005) (0)
- Local Representation of N -Body Coulomb Energy with Path Integrals (2014) (0)
- Photoswitchable Drugs and Insulin Release: Molecular Events in EPAC2A Protein (2018) (0)
- 1PT130 Molecular dynamics simulations of endo-1,3-β-glucanase and oligosaccharide complex(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- Activities of PDBj and wwPDB : A new PDB format, Data Deposition, Validation, and Data Integration(PDBj: Protein Data Bank Japan,The 51st Annual Meeting of the Biophysical Society of Japan) (2013) (0)
- 1P127 Zero-dipole summation method for evaluating electrostatic interaction in molecular simulation of biomolecular system(06.Electronic state,Poster,The 51st Annual Meeting of the Biophysical Society of Japan) (2013) (0)
- 3P112 A theoretical approach to a novel proton transfer pathway of cytochrome c oxidase(Electronic states,Poster Presentations) (2007) (0)
- [New progress in crystallization technology of membrane protein and introduction of pharamaceutical innovation value chain]. (2008) (0)
- Bioinformatics in Japan Development and Maintenance of PDBj as a Member of wwPDB (2007) (0)
- Energy landscape of helical peptides in water (2001) (0)
- Analysis of the free energy landscape of a peptide molecule (2001) (0)
- Aquaporin1 channel proteins : Hybrid-QM/MM Computer Simulation (2003) (0)
- 1P579 Large-scale molecular dynamics simulations with the pairwise electrostatic interaction method for protein-solvent systems(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 1P571 A Computational Study of Monoamine Oxidase A Dynamics(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 1C1412 Toward a simplified screening method using a novel VanX cell lysis activity(Proteins: Measurement, Analysis, Engineering,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- 1P055 QM/MM study on catalytic mechanism of PPIase protein Pin1(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- OneDep: unified wwPDB system for deposition, biocuration and validation of macromolecular structures in the PDB archive (2017) (0)
- 3P356 New data deposition website "ADIT-NMR" of BMRB as a biological macro molecular NMR database(Others,Poster Presentations) (2007) (0)
- 2P035 1G1535 Distinct roles of buried and exposed interface residues in selection of multiple partners by date hub proteins(The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- 1P-067 Improvement of Sampling Efficiency of Multicanonical Molecular Dynamics by Trivial Parallelization(Protein:Measurement & Analysis, The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- The Trial of Drug Discovery using the In-Silico Screening Methods Developed by Pharmaceutical Innovation Value Chain (2010) (0)
- 2P317 Quantum chemical study of the spin density distribution of the special pair cation radical in the bacterial photosynthetic reaction center(Photobiology-photosynthesis, and vision and photoreception,Oral Presentations) (2007) (0)
- wwPDB OneDep validation services (2017) (0)
- A development of a new method for the ligand-protein docking considering the protein flexibility (2003) (0)
- Density Functional Study of the Origin of the Strongly Delocalized Electronic Structure of the CuA Site in Cytochrome c Oxidase (2012) (0)
- The program Shrike by using the DEE algorithm to design the mutation of proteins (1999) (0)
- AMED-BINDS: Basis for Supporting Innovative Drug Discovery and Life Science Research (2019) (0)
- 2P063 Contact number diffusion model for the normal mode analysis of protein structure(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014)) (2014) (0)
- Editorial (2020) (0)
- 2P008 folding simulation of a 40-residue protein, H-NS, involving alpha and beta secondfary sytuctures in explicit water(Proteins-structure and structure-function relationship,Poster Presentations) (2007) (0)
- Data Curation, Quality Control, and User Services at Protein Data Bank Japan (2005) (0)
- Structural elements responsible for the transition between closed states of inward rectifier K+ channel (2009) (0)
- 2P396 Quantum mechanical study of the proton transfer via a peptide bond in the novel pathway of proton translocation of cytochrome c oxidase(45. Electronic structure,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- Correction of the classical free energy landscapes of peptide conformations by quantum mechanical calculations. (2000) (0)
- Model Building Study of Complex Structures Using NMR Shift Change Information (2006) (0)
- Free energy landscape of proline cis-trans isomerization. (1999) (0)
- 1P021 Conformational transitions in the CDRH3 region of the antidansyl monoclonal antibody by molecular dynamics simulations(Protein:Structure,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- Synthesis and Characterization of Collagenous Peptides Cross-Linked at Their Amino and Carboxy Termini (1996) (0)
- A Similarity Search UsingMolecular Topological Graphs (2014) (0)
- Structural Approach to the molecular recognition of proteins. (2000) (0)
- 2P099 Study on the interaction of pi-electron of Benzene and Water molecule using QM/MM simulation (2005) (0)
- 3B1010 Molecular dynamics simulations of dynein motor domain in explicit water(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
- Pattern recognition for Protein three-dimensional structures : Similarity search of protein folds, local atomic arrangements, and molecular surfaces (2008) (0)
- 1P007 Free-energy landscape of a 10-residue peptide obtained from multicanomical molecular dynamics simulation and its calibration method (2005) (0)
- 2S1-6 Expect for Database Center for Life Science(2S1 Activities of Database Center for Life Science,The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Omokage Search and Gmfit: Shape Similarity Search and Superposition among Models and Maps (2016) (0)
- A patient with a rupture of cystic adenomyosis who underwent enucleation by laparoscopy for acute abdomen (2016) (0)
- Data Science and PDBj Activities (2018) (0)
- Web servers for multiscale structures by cryo-EM and other methods (2017) (0)
- 30p-E-3 Spin Freezing in Geometrically Frustrated β-Mn (1999) (0)
- Educational Outreach and User Training at the Worldwide Protein Data Bank (2014) (0)
- 1P-003 Viewing 3D electron microscopy data by EM Navigator(Protein:Structure, The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
- PDB-ML, an XML for Protein Data Bank, and a search system with it (2003) (0)
- 1P481 Real-time Structure Based Queries at the Protein Data Bank japan(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- Conformational prediction of a fragment peptide of EGF receptor and the verification by the experimental data (1999) (0)
- A Simple Efficient Molecular Dynamics Scheme for Evaluating Electrostatic Interaction of Particle Systems (2008) (0)
- 1P081 Evaluation of AmossPresto, a newly developed system of QM/MM hybrid molecular dynamics simulation (2004) (0)
- Side-chain Conformations Cooperatively Restricted in Protein Secondary Structure (1996) (0)
- COMPUTERS IN ANALYSIS, MOLECULAR MODELLING AND MOLECULAR DESIGN C170 (2005) (0)
- Editorial (2020) (0)
- Black holes submerged in Anti-de Sitter space (2018) (0)
- Biocuration of experimentally-determined 3D macromolecular structures and their complexes at the wwPDB (2017) (0)
- Development of a new local drug delivery system for the uterus using bio-nanocapsule (2015) (0)
- Nearsightedness of Finite Homogeneous Model Systems (2015) (0)
- 2P449 Improvement of the method for discriminating between biological and crystal-packing contacts in protein crystals(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006) (0)
- 3P-107 Quantum chemical studies of electronic structures and chemical indices of the active site of metalloprotein : Application to Hemerythrin(The 46th Annual Meeting of the Biophysical Society of Japan) (2008) (0)
- Metal Ion Induced Self-Assembly of a Designed Three Helix Bundle (1998) (0)
- 1P024 Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families(Protein:Structure,The 48th Annual Meeting of the Biophysical Society of Japan) (2010) (0)
- Structural models ofribonuclease H domains inreverse transcriptases fromretroviruses (1991) (0)
- Molecular dynamics equation designed for realizing arbitrary density: application to sampling method utilizing the Tsallis generalized distribution (2010) (0)
- Calculation of electrostatic interactions by zero-multipole summation method: theory and practice in molecular simulation (2016) (0)
- Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes (2012) (0)
- In-vitro and in-silico studies of ligand binding to the nuclear receptor PPARgamma using FRET and MD (2015) (0)
- Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix (2023) (0)
- Announcement of new Editorial Board members (2022) (0)
- Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins (2016) (0)
- Big data science at AMED-BINDS (2020) (0)
- Foreword to ‘Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines’, a special issue in Honour of Fumio Arisaka’s 70th birthday (2018) (0)
- Quality of therapy and mental health among occupational therapists during the COVID-19 pandemic (2022) (0)
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What Schools Are Affiliated With Haruki Nakamura?
Haruki Nakamura is affiliated with the following schools:
