Yasuomi Kiyota
A5019968746- Protein Structure and Dynamics
- Hemoglobin structure and function
- Mass Spectrometry Techniques and Applications
- Spectroscopy and Quantum Chemical Studies
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Analytical Chemistry and Chromatography
- DNA and Nucleic Acid Chemistry
- thermodynamics and calorimetric analyses
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- Photochemistry and Electron Transfer Studies
- RNA and protein synthesis mechanisms
- vaccines and immunoinformatics approaches
- Cancer-related gene regulation
- Plant-based Medicinal Research
- Biofield Effects and Biophysics
- S100 Proteins and Annexins
- Electrochemical Analysis and Applications
- Ion channel regulation and function
- Quantum, superfluid, helium dynamics
- HER2/EGFR in Cancer Research
- Photosynthetic Processes and Mechanisms
- Microbial Fuel Cells and Bioremediation
- CO2 Reduction Techniques and Catalysts
Kitasato University
2014-2024
Institute for Molecular Science
2009-2011
Okazaki National Research Institutes
2008-2010
The Graduate University for Advanced Studies, SOKENDAI
2010
Ritsumeikan University
2009
Kyoto University
2007-2008
Abstract We present the results for CAPRI Round 54, 5th joint CASP‐CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21 941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified...
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
CO escaping pathways of Myoglobin were investigated in terms 3D distribution function which was calculated by the 3D-RISM theory. The partial molar volume changes through show excellent agreement with those from experiment.
A new approach to investigate a molecular recognition process of protein is presented based on the three-dimensional reference interaction site model (3D-RISM) theory, statistical mechanics theory liquids. Numerical procedure for solving conventional 3D-RISM equation consists two steps. In step 1, we solve ordinary RISM (or 1D-RISM) equations solvent mixture including target ligands in order obtain density pair correlation functions (PCF) among molecules solution. Then, solute-solvent system...
Abstract Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state art in computing protein structure from sequence. In spring 2020, CASP launched a community project to compute structures most structurally challenging proteins coded for SARS‐CoV‐2 genome. Forty‐seven research groups submitted over 3000 three‐dimensional models and 700 sets accuracy estimates on 10 proteins. The resulting were released public. members also worked together provide...
We present the results for CAPRI Round 54, 5th joint CASP-CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homo-dimers, 3 homo-trimers, 13 hetero-dimers antibody-antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified a...
Ca2+-binding proteins are widely distributed throughout cells and play various important roles. Calbindin D9k is a member of the EF-hand protein family. In this study, we examined binding Ca2+ to calbindin in terms free energy solvation, as obtained by 3D reference interaction site model theory, which describes statistical mechanics liquids. We also investigated main structural biological factor using spatial decomposition analysis solvation values decomposed into residue. found some...
Abstract In this article, we present the multicore (mc) QM/MM method, a method that can optimize structure of chromophore aggregate in protein. A QM region is composed sum subregions are small enough to apply practical electronic calculations. energy gradient calculations performed for each subregion. Several benchmark examinations were carried out figure availabilities and limitations. interregion distances more than 3.5–4.0 Å, mcQM/MM very close obtained by ordinary which all treated...
Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular in which one or several guest molecules are bound with high probability at particular site such cleft cavity, of host molecule orientation. It thermodynamic characterised by the difference free energies between two states host–guest system, and unbound. The features extremely heterogeneous atomic-environment around binding sites, has turned away...
Abstract To gain a detailed understanding of protein structure, function, and interaction, water molecules around proteins are important. Therefore, computational methods for predicting positions required. When hydration distribution such as 3D function is available, to predict explicitly from the useful. In this paper, we introduce DroPred, method based on oxygen atoms using weighted Monte Carlo method. The probability density derived used weight in DroPred generates multiple samples single...
Recent progress in the theory of molecular recognition biomolecules is reviewed, which has been made based on statistical mechanics liquids or 3D-RISM/RISM theory. The a ligand by protein realized 3D-distribution functions: if one finds some conspicuous peaks distribution inside protein, then regarded as “recognized” protein. functions can be obtained means Some biochemical processes are investigated, intimately related to small ligands such water, ions, and carbon monoxide
The activation of epidermal growth factor receptor (EGFR) involves the geometrical conversion extracellular domain (ECD) from tethered to extended forms with dynamic rearrangement relative positions four subdomains (SDs); however, this process has not yet been thoroughly understood. We compare two different X-ray crystal structures ECD and simulate using adiabatic mapping that combines normal mode analysis elastic network model (ENM-NMA) energy optimization. A comparison reveals rigidity...