Yasuomi Kiyota

ORCID: 0000-0003-2805-1769
Publications
Citations
Views
---
Saved
---
About
Contact & Profiles
Research Areas
  • 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

Marc F. Lensink Guillaume Brysbaert Nessim Raouraoua Paul A. Bates Marco Giulini and 95 more Rodrigo V. Honorato Charlotte van Noort João M. C. Teixeira Alexandre M. J. J. Bonvin Ren Kong Hang Shi Xufeng Lu Shan Chang Jian Liu Zhiye Guo Xiao Chen Alex Morehead Raj S. Roy Tianqi Wu Nabin Giri Farhan Quadir Chen Chen Jianlin Cheng Carlos A. Del Carpio Eichiro Ichiishi Luis Ángel Rodríguez-Lumbreras Juan Fernández‐Recio Ameya Harmalkar Lee‐Shin Chu Samuel W. Canner Rituparna Smanta Jeffrey J. Gray Hao Li Peicong Lin Jiahua He Huanyu Tao Sheng‐You Huang Jorge Roel‐Touris Brian Jiménez‐García Charles Christoffer Anika Jain Yuki Kagaya Harini Kannan Tsukasa Nakamura Genki Terashi Jacob Verburgt Yuanyuan Zhang Zicong Zhang Hayato Fujuta Masakazu Sekijima Daisuke Kihara Omeir Khan Sergei Kotelnikov Usman Ghani Dzmitry Padhorny Dmitri Beglov Sándor Vajda Dima Kozakov Surendra S. Negi Tiziana Ricciardelli Didier Barradas‐Bautista Zhen Cao Mohit Chawla Luigi Cavallo Romina Oliva Rui Yin Melyssa Cheung Johnathan D. Guest Jessica Lee Brian G. Pierce Ben Shor Tomer Cohen Matan Halfon Dina Schneidman‐Duhovny Shaowen Zhu Rujie Yin Yuanfei Sun Yang Shen Martyna Maszota‐Zieleniak Krzysztof K. Bojarski Emilia A. Lubecka Mateusz Marcisz Annemarie Danielsson Łukasz Dziadek Margrethe Gaardløs Artur Giełdoń Adam Liwo Sergey A. Samsonov Rafał Ślusarz Karolina Zięba Adam K. Sieradzan Cezary Czaplewski Shinpei Kobayashi Yuta Miyakawa Yasuomi Kiyota Mayuko Takeda‐Shitaka Kliment Olechnovič Lukas Valančauskas Justas Dapkūnas Česlovas Venclovas

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...

10.1002/prot.26609 article EN cc-by Proteins Structure Function and Bioinformatics 2023-10-31
Marc F. Lensink Guillaume Brysbaert Théo Mauri Nurul Nadzirin Sameer Velankar and 95 more Raphaël A. G. Chaleil Tereza Clarence Paul A. Bates Ren Kong Bin Liu Guangbo Yang Ming Liu Hang Shi Xufeng Lu Shan Chang Raj S. Roy Farhan Quadir Jian Liu Jianlin Cheng Anna Antoniak Cezary Czaplewski Artur Giełdoń Mateusz Kogut Agnieszka G. Lipska Adam Liwo Emilia A. Lubecka Martyna Maszota‐Zieleniak Adam K. Sieradzan Rafał Ślusarz Patryk A. Wesołowski Karolina Zięba Carlos Adriel Del Carpio Munoz Eiichiro Ichiishi Ameya Harmalkar Jeffrey J. Gray Alexandre M. J. J. Bonvin Francesco Ambrosetti Rodrigo V. Honorato Zuzana Jandová Brian Jiménez‐García Panagiotis I. Koukos Siri van Keulen Charlotte W. van Noort Manon Réau Jorge Roel‐Touris Sergei Kotelnikov Dzmitry Padhorny Kathryn A. Porter Andrey Alekseenko Mikhail Ignatov Israel Desta Ryota Ashizawa Zhuyezi Sun Usman Ghani Nasser Hashemi Sándor Vajda Dima Kozakov Mireia Rosell Luis Ángel Rodríguez-Lumbreras Juan Fernández‐Recio Agnieszka Karczyńska Sergei Grudinin Yumeng Yan Hao Li Peicong Lin Sheng‐You Huang Charles Christoffer Genki Terashi Jacob Verburgt Daipayan Sarkar Tunde Aderinwale Xiao Wang Daisuke Kihara Tsukasa Nakamura Yuya Hanazono Ragul Gowthaman Johnathan D. Guest Rui Yin Ghazaleh Taherzadeh Brian G. Pierce Didier Barradas‐Bautista Zhen Cao Luigi Cavallo Romina Oliva Yuanfei Sun Shaowen Zhu Yang Shen Taeyong Park Hyeonuk Woo Jinsol Yang Sohee Kwon Jonghun Won Chaok Seok Yasuomi Kiyota Shinpei Kobayashi Yoshiki Harada Mayuko Takeda‐Shitaka Petras J. Kundrotas Amar Singh Ilya A. Vakser

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....

10.1002/prot.26222 article EN Proteins Structure Function and Bioinformatics 2021-08-28

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.

10.1021/ja900332e article EN Journal of the American Chemical Society 2009-03-02

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...

10.1021/ct200358h article EN Journal of Chemical Theory and Computation 2011-10-04

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...

10.1002/prot.26231 article EN publisher-specific-oa Proteins Structure Function and Bioinformatics 2021-08-31
Marc F. Lensink Guillaume Brysbaert Nessim Raouraoua Paul A. Bates Marco Giulini and 95 more Rodrigo V. Honorato Charlotte van Noort João M. C. Teixeira Alexandre M. J. J. Bonvin Ren Kong Hang Shi Xufeng Lu Shan Chang Jian Liu Zhiye Guo Xiao Chen Alex Morehead Raj S. Roy Tianqi Wu Nabin Giri Farhan Quadir Chen Chen Jianlin Cheng Carlos Del Carpio Eichiro Ichiishi Luis Ángel Rodríguez-Lumbreras Juan Fernández‐Recio Ameya Harmalkar Lee‐Shin Chu Samuel W. Canner Rituparna Smanta Jeffrey J. Gray Hao Li Peicong Lin Jiahua He Huanyu Tao Sheng‐You Huang Jorge Roel Brian Jiménez‐García Charles Christoffer Anika Jain J Yuki Kagaya Harini Kannan Tsukasa Nakamura Genki Terashi Jacob Verburgt Yuanyuan Zhang Zicong Zhang Hayato Fujuta Masakazu Sekijima Daisuke Kihara Omeir Khan Sergei Kotelnikov Usman Ghani Dzmitry Padhorny Dmitri Beglov Sándor Vajda Dima Kozakov Surendra Negi S Tiziana Ricciardelli Didier Barradas‐Bautista Zhen Cao Mohit Chawla Luigi Cavallo Romina Oliva Rui Yin Melyssa Cheung Johnathan D. Guest Jessica Lee Brian G. Pierce Ben Shor Tomer Cohen Matan Halfon Dina Schneidman‐Duhovny Shaowen Zhu Rujie Yin Yuanfei Sun Yang Shen Martyna Maszota‐Zieleniak Krzysztof Bojarski K Emilia A. Lubecka Mateusz Marcisz Annemarie Danielsson Łukasz Dziadek Margrethe Gaardløs Artur Giełdoń Adam Liwo Sergey A. Samsonov Rafał Ślusarz Karolina Zięba Adam K. Sieradzan Cezary Czaplewski Shinpei Kobayashi Yuta Miyakawa Yasuomi Kiyota Mayuko Takeda‐Shitaka Kliment Olechnovič Lukas Valančauskas Justas Dapkūnas Česlovas Venclovas

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...

10.22541/au.168888815.53957253/v1 preprint EN cc-by Authorea (Authorea) 2023-07-09

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...

10.1021/jp504822r article EN The Journal of Physical Chemistry B 2014-09-24

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...

10.1002/jcc.21156 article EN Journal of Computational Chemistry 2008-11-13

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...

10.1080/0144235x.2011.648755 article EN International Reviews in Physical Chemistry 2011-10-01

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...

10.1093/bulcsj/uoae063 article EN cc-by-nc Bulletin of the Chemical Society of Japan 2024-06-01

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

10.2142/biophys.51.222 article EN Seibutsu Butsuri 2011-01-01

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...

10.1248/cpb.c19-00205 article EN Chemical and Pharmaceutical Bulletin 2019-09-30
Coming Soon ...