Papers

• R. Toyooka, S. Nishimoto, T. Tendo, T. Horiyama*, T. Tachi*, and Y. Matsunaga*, “Explicit description of viral capsid subunit shapes by unfolding dihedrons” Communications Biology 7, 1509 (9 pages) (2024) DOI:10.1038/s42003-024-07218-x

• J. Jung, K. Yagi, C. Tan, H. Oshima, T. Mori, I. Yu, Y. Matsunaga, C. Kobayashi, S. Ito, D. Ugarte La Torre, and Y. Sugita* “GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models” Journal of Physical Chemistry B 128, 6028-6048 (2024) DOI:10.1021/acs.jpcb.4c02096

• T. Ishizone*, Y. Matsunaga, S. Fuchigami, and K. Nakamura “Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior” Journal of Chemical Theory and Computation 20, 436-450 (2023) DOI:10.1021/acs.jctc.3c01025

• 松永康佑、東田連 “gRESTシミュレーションによるVHH抗体の構造サンプリング” 理論化学会会誌「フロンティア」 1月号(通巻17号), 13-22 (2023)

• Y. Matsunaga*, S. Fuchigami, T. Ogane, and S. Takada “End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images”, Scientific Reports 13, 129 (16 pages) (2023) DOI:10.1038/s41598-022-27057-2

• T. Ogane, D. Noshiro, T. Ando, A. Yamashita, Y. Sugita, and Y. Matsunaga* “Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images”, PLoS Computational Biology 18, e1010384 (23 pages) (2022) DOI:10.1371/journal.pcbi.1010384

• Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugia* “Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation”, Biophysical Reviews 14, 1503-1512 (2022) DOI:10.1007/s12551-022-01030-9

• T. Murakami, S. Kumachi, Y. Matsunaga, M. Sato, K. Wakabayashi-Nakao, H. Masaki, R. Yonehara, M. Motohashi, N. Nemoto, and M. Tsuchiya* “Construction of a Humanized Artificial VHH Library Reproducing Structural Features of Camelid VHHs for Therapeutics”, Antibodies 11, 10 (18 pages) (2022) DOI:10.3390/antib11010010

• R. Higashida, Y. Matsunaga* “Enhanced Conformational Sampling of Nanobody CDR H3 Loop by Generalized Replica-Exchange with Solute Tempering”, Life 11, 1428 (13 pages) (2021) DOI:10.3390/life11121428

• 松永康佑、藤崎弘士*、森次圭 “タンパク質の構造変化をどのように記述するか――生体分子におけるパスサンプリング手法の発展” 日本物理学会誌 76巻11号, 714-722 (2021)

• C. Kobayashi, Y. Matsunaga, J. Jung, Y. Sugita* “Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca2+-ATPase”, Proceeding of the National Academy of Sciences of the United States of America 118, e2105507118 (8 pages) (2021) DOI:10.1073/pnas.2105507118

• T. Niina, Y. Matsunaga, and S. Takada* “Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure”, PLoS Computational Biology 17, e1009215 (24 pages) (2021) DOI:10.1371/journal.pcbi.1009215

• A. Shinobu, C. Kobayashi, Y. Matsunaga, and Y. Sugita* “Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins”, Journal of Chemical Information and Modeling 61, 2427–2443 (2021) DOI:10.1021/acs.jcim.1c00286

• Y. Matsunaga, and Y. Sugita* “Use of single-molecule time-series data for refining conformational dynamics in molecular simulations”, Current Opinion in Structural Biology 61, 153-159 (2020) DOI:10.1016/j.sbi.2019.12.022

• A. Shinobu, C. Kobayashi, Y. Matsunaga, and Y. Sugita* “Building a macro-mixing dual‑basin Gō model using the Multistate Bennett Acceptance Ratio”, Biophysics and Physicobiology 16, 310-321 (2019) DOI:10.2142/biophysico.16.0_310

• 松永康佑* “全原子分子動力学シミュレーションが解き明かす多剤排出トランスポーターAcrBの薬剤排出機構” 生物物理 59巻2号, 084-087 (2019) DOI:10.2142/biophys.59.084

• H. Fujisaki*, K. Moritsugu, and Y. Matsunaga “Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions”, International Journal of Molecular Sciences 19, 3177 (19 pages) (2018)

• Y. Matsunaga, and Y. Sugita*, “Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning”, eLife 7, e32668 (19 pages) (2018) (日本語による解説 「1分子計測のデータ同化による生体分子構造ダイナミクス －小タンパク質が折り畳まれる際の中間構造・パスウェイを特定－」)

• Y. Matsunaga, and Y. Sugita*, “Refining Markov State Models for conformational dynamics using ensemble-averaged data and time-series trajectories”, The Journal of Chemical Physics 148, 241731 (7 pages) (2018) Selected as a 2018 Editors’ Choice article

• Y. Matsunaga*, T. Yamane, T. Terada, K. Moritsugu, H. Fujisaki, S. Murakami, M. Ikeguchi, and A. Kidera, “Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB”, eLife 7, e31715 (19 pages) (2018) (日本語による解説 「多剤排出トランスポーターの薬剤排出機構を解明 －スーパーコンピュータ「京」で巨大分子機械の動きを計算－」)

• C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita*,"GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms", Journal of Computational Chemistry 38, 2193-2206 (2017)

• Y. Matsunaga, Y. Komuro, C. Kobayashi, J. Jung, T. Mori, and Y. Sugita*, “Dimensionality of Collective Variables for Describing Conformational Changes of a Multi-Domain Protein” The Journal of Physical Chemistry Letters 7, 1446–1451 (2016)

• C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita*, “Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins” The Journal of Physical Chemistry B 119, 14584-14593 (2015)

• H. Fujisaki, K. Moritsugu, Y. Matsunaga, T. Morishita, and L. Maragliano*, “Extended phase-space methods for enhanced sampling in molecular simulations: a review” Frontiers in Bioengineering and Biotechnology 3, Article 125 (10 pages) (2015)

• Y. Matsunaga, A. Kidera, and Y. Sugita*, “Sequential data assimilation for single-molecule FRET photon-counting data” The Journal of Chemical Physics 142, 214115 (12 pages) (2015)

• J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita*, “GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations” WIREs Computational Molecular Science 5, 310-323 (2015) (日本語による解説 「超並列分子動力学計算ソフトウェア「GENESIS」を開発 －「京」を活用し巨大生体分子システムのシミュレーションを実現－」)

• 松永康佑* “ストリング法によるタンパク質構造変化の解析” 統計数理 62, 285-299 (2014)

• 松永康佑* “ストリング法によるタンパク質構造変化の解析” 分子シミュレーション研究会会誌 アンサンブル 16, 29-35 (2014)

• Y. Matsunaga, A. Baba, C.-B. Li, J. E. Straub, M. Toda, T. Komatsuzaki, and R. S. Berry, “Spatio-temporal hierarchy in the dynamics of a minimalist protein model” The Journal of Chemical Physics 139, 215101 (13 pages) (2013)

• Y. Matsunaga, R. Koike, M. Ota, J. H. Tame, and A. Kidera, “Influence of Structural Symmetry on Protein Dynamics” PLoS ONE 7, e50011 (11 pages) (2012)

• Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera, “Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase” PLoS Computational Biology 8, e1002555 (12 pages) (2012)

• S. Fuchigami, H. Fujisaki, Y. Matsunaga, and A. Kidera, “Protein Functional Motions: Basic Concepts and Computational Methodologies” Advances in Chemical Physics 145, 35-82 (2011)

• D. M. Leitner, Y. Matsunaga, C.-B. Li, T. Komatsuzaki, A. Shojiguchi, and M. Toda, “Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics” Advances in Chemical Physics 145, 83-122 (2011)

• Y. Matsunaga, C.-B. Li, and T. Komatsuzaki, “Cooperativity at different space and time scales in multiscale protein dynamics” Physical Review E 82, 016213 (12 pages) (2010)

• Y. Matsunaga, S. Fuchigami, and A. Kidera, “Multivariate Frequency Domain Analysis of Protein Dynamics” The Journal of Chemical Physics 130, 124104 (8 pages) (2009)

• Y. Matsunaga, C.-B. Li and T. Komatsuzaki, “Anomalous Diffusion in Folding Dynamics of Minimalist Protein Landscape” Physical Review Letters 99, 238103 (4 pages) (2007)

• G. J. Rylance, R. L. Johnston, Y. Matsunaga, C.-B. Li, A. Baba and T. Komatsuzaki, “Topographical complexity of multidimensional energy landscapes” Proceedings of the National Academy of Sciences U.S.A. 103, 18551-18555 (2006)

• C.-B. Li, Y. Matsunaga, M. Toda and T. Komatsuzaki, “Phase Space Reaction Network on a Multisaddle Energy Landscape: HCN isomerization” The Journal of Chemical Physics 123, 184301 (13 pages) (2005)

• T. Komatsuzaki, K. Hoshino, Y. Matsunaga, G. J. Rylance, R. L. Johnston, and D. J. Wales, “How Many Dimensions are Required to Approximate the Potential Energy Landscape of a Model Protein?” The Journal of Chemical Physics 122, 084714 (9 pages) (2005)

• T. Komatsuzaki, K. Hoshino, and Y. Matsunaga, “Regularity in Chaotic Transitions on Multibasin Landscapes” Advances in Chemical Physics 130B, 257-313 (2005)

• 松永康佑 “蛋白質フォールディングのダイナミックス -異常拡散と動的相関-“ 物性研究 81, 571-592 (2004) (2002年度物性研究修士論文募集で審査の上、採択・掲載)

• 小松崎民樹、松永康佑 “タンパク質フォールディングのダイナミックス -異常拡散と階層的規則性-“ 生物物理 42, 285 (2002)

• Y. Matsunaga, K. S. Kostov, and T. Komatsuzaki, “Multibasin Dynamics in Off-Lattice Minimalist Protein Landscapes” The Journal of Physical Chemistry A 106, 10898-10907 (2002)

Proceedings

• K. Hoshino, Y. Matsunaga, M. Miller, D. J. Wales, and T. Komatsuzaki, “A Coarse-Graining of Energy Landscapes of Proteins -Structural Stability of the Most Stable States-“ AIP conference series for Slow Dynamics in Complex Systems 708, 344-345 (2004)

• Y. Matsunaga and T. Komatsuzaki, “Protein Folding Dynamics: Ergodic Behavior in Principal Component Space” AIP conference series for Slow Dynamics in Complex Systems 708, 342-343 (2004)

• Y. Matsunaga, K. S. Kostov, and T. Komatsuzaki, “Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes” AIP conference series for Slow Dynamics in Complex Systems 708, 302-305 (2004)

Books

• A. Kidera, K. Moristugu, Y. Matsunaga, and H. Fujisaki, “Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics” Proteins: Energy, Heat and Signal Flow, Chapter 5, p107-127 (2009), CRC Press.

Others

• 松永康佑 “理論系から見た分子集合体の機能設計 ―タンパク質の機能ダイナミクス” 日本化学会 第二次先端ウォッチング調査：融合領域の創成, 31-34 (2019)

• 松永康佑 “スーパーコンピューター「京」によって解明された多剤排出トランスポーターの薬剤排出機構” バイオサイエンスとインダストリー 76, 410-412 (2018)

• 松永康佑 “実験と計算の時間スケールが重なったことで見えてきたこと” 蛋白質科学会アーカイブ http://www.pssj.jp/archives/essay/Es_05/Es_05.html

• 松永康佑 “SC09参加報告” http://www.nsc.riken.jp/SC/SC09/Matsunaga.pdf (次世代スーパーコンピューティングシンポジウム2009におけるポスター発表優秀賞受賞の副賞としてのSC09参加の際に依頼執筆したもの)

• 松永康佑、小松崎民樹 “高分子とカオス -異常拡散と階層的規則性-“ 高分子 57, 58-61 (2008)

• 星野恭子、松永康佑、G. J. Rylance、R. L. Johnston、D. J. Wales、小松崎民樹 “タンパク質エネルギー地形における構造多様性と多次元エネルギー地形の新しい可視化手法” 物性研究 86-1, 117-122 (2006)

• 松永康佑 “蛋白質折れ畳みダイナミックスにおける階層的規則性” 物性研究 78, 457 (2002)