Yuji Sugita

17.0k total citations · 3 hit papers
269 papers, 13.0k citations indexed

About

Yuji Sugita is a scholar working on Molecular Biology, Materials Chemistry and Atomic and Molecular Physics, and Optics. According to data from OpenAlex, Yuji Sugita has authored 269 papers receiving a total of 13.0k indexed citations (citations by other indexed papers that have themselves been cited), including 195 papers in Molecular Biology, 64 papers in Materials Chemistry and 53 papers in Atomic and Molecular Physics, and Optics. Recurrent topics in Yuji Sugita's work include Protein Structure and Dynamics (137 papers), Enzyme Structure and Function (57 papers) and Spectroscopy and Quantum Chemical Studies (42 papers). Yuji Sugita is often cited by papers focused on Protein Structure and Dynamics (137 papers), Enzyme Structure and Function (57 papers) and Spectroscopy and Quantum Chemical Studies (42 papers). Yuji Sugita collaborates with scholars based in Japan, United States and South Korea. Yuji Sugita's co-authors include Yuko Okamoto, Michael Feig, Ayori Mitsutake, Takaharu Mori, Suyong Re, Jaewoon Jung, Takao Yoda, Chigusa Kobayashi, Chikashi Toyoshima and Naoyuki Miyashita and has published in prestigious journals such as Nature, Proceedings of the National Academy of Sciences and Journal of the American Chemical Society.

In The Last Decade

Yuji Sugita

263 papers receiving 12.8k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Replica-exchange molecular dynamics method for protein folding

1999 3.6k citations Yuji Sugita, Yuko Okamoto profile →
Generalized-ensemble algorithms for molecular simulations of biopolymers

2001 651 citations Yuji Sugita, Yuko Okamoto et al. profile →
Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

2020 298 citations Takaharu Mori, Yuji Sugita et al. profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Yuji Sugita Japan	52	9.3k	2.9k	2.1k	1.5k	1.1k	269	13.0k
Haruki Nakamura Japan	63	11.5k 1.2×	3.0k 1.0×	1.5k 0.7×	1.3k 0.9×	1.0k 0.9×	472	15.7k
Yong Duan United States	41	10.5k 1.1×	3.1k 1.1×	1.8k 0.8×	1.5k 1.0×	500 0.4×	197	14.8k
Rosemary Braun United States	20	10.1k 1.1×	2.4k 0.8×	1.9k 0.9×	1.1k 0.7×	470 0.4×	46	15.8k
M Abraham Australia	6	9.5k 1.0×	2.8k 1.0×	1.6k 0.8×	1.1k 0.7×	662 0.6×	6	18.2k
Sunhwan Jo United States	34	12.6k 1.3×	1.5k 0.5×	1.5k 0.7×	1.1k 0.8×	767 0.7×	69	17.0k
Ray Luo United States	43	12.6k 1.3×	3.3k 1.1×	2.1k 1.0×	1.6k 1.0×	612 0.5×	180	17.5k
Alexey V. Onufriev United States	37	13.7k 1.5×	3.4k 1.1×	2.4k 1.1×	1.5k 1.0×	669 0.6×	100	19.0k
Henk Bekker Netherlands	11	9.0k 1.0×	2.5k 0.9×	1.9k 0.9×	1.1k 0.7×	500 0.4×	20	15.5k
David J. States United States	32	13.9k 1.5×	3.7k 1.3×	2.6k 1.2×	3.0k 2.0×	756 0.7×	75	20.1k
J. G. E. M. Fraaije Netherlands	26	9.0k 1.0×	4.3k 1.5×	2.0k 1.0×	1.1k 0.7×	491 0.4×	84	17.4k

Countries citing papers authored by Yuji Sugita

Since Specialization

Citations

This map shows the geographic impact of Yuji Sugita's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Yuji Sugita with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Yuji Sugita more than expected).

Fields of papers citing papers by Yuji Sugita

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Yuji Sugita. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Yuji Sugita. The network helps show where Yuji Sugita may publish in the future.

Co-authorship network of co-authors of Yuji Sugita

This figure shows the co-authorship network connecting the top 25 collaborators of Yuji Sugita. A scholar is included among the top collaborators of Yuji Sugita based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Yuji Sugita. Yuji Sugita is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

Monego, Debora, et al.. (2025). ColBuilder: flexible structure generation of crosslinked collagen fibrils. Bioinformatics. 41(6).

Niitsu, Ai, Andrew R. Thomson, Jason T. Sengel, et al.. (2025). Rational Design Principles for De Novo α-Helical Peptide Barrels with Dynamic Conductive Channels. Journal of the American Chemical Society. 147(14). 11741–11753. 2 indexed citations

Re, Suyong, et al.. (2024). Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proceedings of the National Academy of Sciences. 121(15). e2317197121–e2317197121. 1 indexed citations

Takada, Shoji, et al.. (2023). Extension of the iSoLF implicit-solvent coarse-grained model for multicomponent lipid bilayers. The Journal of Chemical Physics. 159(7). 3 indexed citations

Tan, Cheng, Ai Niitsu, & Yuji Sugita. (2023). Highly Charged Proteins and Their Repulsive Interactions Antagonize Biomolecular Condensation. JACS Au. 3(3). 834–848. 20 indexed citations

Niitsu, Ai & Yuji Sugita. (2023). Towards de novo design of transmembrane α-helical assemblies using structural modelling and molecular dynamics simulation. Physical Chemistry Chemical Physics. 25(5). 3595–3606. 7 indexed citations

Dokainish, Hisham & Yuji Sugita. (2022). Structural effects of spike protein D614G mutation in SARS-CoV-2. Biophysical Journal. 122(14). 2910–2920. 9 indexed citations

Dokainish, Hisham, Suyong Re, Takaharu Mori, et al.. (2022). The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein. eLife. 11. 44 indexed citations

Mori, Takaharu, Genki Terashi, Daisuke Matsuoka, Daisuke Kihara, & Yuji Sugita. (2021). Efficient Flexible Fitting Refinement with Automatic Error Fixing for De Novo Structure Modeling from Cryo-EM Density Maps. Journal of Chemical Information and Modeling. 61(7). 3516–3528. 11 indexed citations

10.

Re, Suyong, Grzegorz Nawrocki, Hiraku Oshima, et al.. (2021). Reduced efficacy of a Src kinase inhibitor in crowded protein solution. Nature Communications. 12(1). 4099–4099. 26 indexed citations

11.

Kato, Naoki, Suyong Re, Kohei Watanabe, et al.. (2021). Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons**. Angewandte Chemie. 133(41). 22575–22584. 1 indexed citations

12.

Kato, Naoki, Suyong Re, Kohei Watanabe, et al.. (2021). Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons**. Angewandte Chemie International Edition. 60(41). 22401–22410. 20 indexed citations

13.

Re, Suyong, Yoshiki Yamaguchi, & Yuji Sugita. (2020). Molecular Dynamics Simulation of Glycans. Trends in Glycoscience and Glycotechnology. 32(188). E113–E118. 6 indexed citations

14.

Kuroki, Kimiko, Naoyuki Miyashita, Mitsunori Shiroishi, et al.. (2019). Structural and Functional Basis for LILRB Immune Checkpoint Receptor Recognition of HLA-G Isoforms. The Journal of Immunology. 203(12). 3386–3394. 34 indexed citations

15.

Feig, Michael, Grzegorz Nawrocki, Isseki Yu, Po-Hung Wang, & Yuji Sugita. (2018). Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments. Journal of Physics Conference Series. 1036. 12010–12010. 22 indexed citations

16.

Yu, Isseki, Takaharu Mori, Tadashi Ando, et al.. (2016). Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm. eLife. 5. 226 indexed citations

17.

Yoda, Takao, Yuji Sugita, & Yuko Okamoto. (2010). Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations. Biophysical Journal. 99(5). 1637–1644. 38 indexed citations

18.

Sugita, Yuji. (2009). Free-energy landscapes of proteins in solution by generalized-ensemble simulations. Frontiers in bioscience. Volume(14). 1292–1292. 2 indexed citations

19.

Sugita, Yuji & Akio Kitao. (1998). Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A. Proteins Structure Function and Bioinformatics. 30(4). 388–400. 31 indexed citations

20.

Sugita, Yuji, et al.. (1994). Recombinant soluble CD59 inhibits reactive haemolysis with complement.. PubMed Central. 82(1). 34–41. 59 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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