World's Best Scientists 2026 revealed!

D-Index & Metrics

Chemistry

D-Index
59
Citations
18446
World Ranking
10001
National Ranking
714

Overview

Yuji Sugita is affiliated with the RIKEN Center for Biosystems Dynamics Research in Japan. Their research spans several areas within biochemistry, genetics, and molecular biology, with a particular focus on molecular biology as a key subfield.

The scientist's work covers a range of topics, including:

  • Protein Structure and Dynamics
  • Enzyme Structure and Function
  • Spectroscopy and Quantum Chemical Studies
  • Bacteriophages and microbial interactions
  • RNA Research and Splicing
  • RNA and protein synthesis mechanisms
  • Genomics and Chromatin Dynamics

Yuji Sugita has published in various notable venues, frequently contributing to:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Biophysical Journal
  • Journal of Chemical Information and Modeling
  • The Journal of Chemical Physics
  • Journal of Chemical Theory and Computation

Some recent publications include:

  • "Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion," 2020, Nature Structural & Molecular Biology
  • "CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations," 2020, Journal of Chemical Theory and Computation
  • "Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein," 2021, Biophysical Journal
  • "New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems," 2020, Journal of Computational Chemistry
  • "The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein," 2022, eLife

Frequent co-authors collaborating with Yuji Sugita include:

  • Jaewoon Jung
  • Chigusa Kobayashi
  • Suyong Re
  • Cheng Tan
  • Kiyoshi Yagi

Their research integrates computational approaches, such as molecular dynamics, with experimental studies in spectroscopy and biophysics to elucidate functional and structural dynamics of biological macromolecules. This multidisciplinary approach supports investigations into protein behavior, enzyme activity, and the mechanisms underlying RNA and protein synthesis.

Best Publications

  • Replica-exchange molecular dynamics method for protein folding

    Yuji Sugita;Yuko Okamoto

  • Generalized-ensemble algorithms for molecular simulations of biopolymers.

    Ayori Mitsutake;Yuji Sugita;Yuko Okamoto

  • Multidimensional replica-exchange method for free-energy calculations

    Yuji Sugita;Akio Kitao;Yuko Okamoto

  • Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion

    Kazuaki Matoba;Tetsuya Kotani;Akihisa Tsutsumi;Takuma Tsuji

  • Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape

    Yuji Sugita;Yuko Okamoto

  • Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

    Isseki Yu;Takaharu Mori;Tadashi Ando;Ryuhei Harada

  • Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+).

    Koji Obara;Naoyuki Miyashita;Cheng Xu;Itaru Toyoshima

  • Crystal structure of α5β1 integrin ectodomain: Atomic details of the fibronectin receptor

    Masamichi Nagae;Suyong Re;Emiko Mihara;Terukazu Nogi

  • Structural basis of Sec-independent membrane protein insertion by YidC

    Kaoru Kumazaki;Shinobu Chiba;Mizuki Takemoto;Arata Furukawa

  • Conformational transition of Sec machinery inferred from bacterial SecYE structures

    Tomoya Tsukazaki;Hiroyuki Mori;Shuya Fukai;Shuya Fukai;Ryuichiro Ishitani

  • Modeling of the inhibitory interaction of phospholamban with the Ca2+ ATPase

    Chikashi Toyoshima;Michio Asahi;Yuji Sugita;Reena Khanna

  • Protein Crowding Affects Hydration Structure and Dynamics

    Ryuhei Harada;Yuji Sugita;Michael Feig;Michael Feig

  • GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

    Jaewoon Jung;Takaharu Mori;Chigusa Kobayashi;Yasuhiro Matsunaga

  • Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT

    Shintaro Doki;Hideaki E. Kato;Nicolae Solcan;Masayo Iwaki

  • GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

    Chigusa Kobayashi;Jaewoon Jung;Yasuhiro Matsunaga;Takaharu Mori

  • Comparisons of force fields for proteins by generalized-ensemble simulations

    Takao Yoda;Yuji Sugita;Yuko Okamoto

  • Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.

    Michael Feig;Isseki Yu;Po Hung Wang;Grzegorz Nawrocki

  • Sarcolipin regulates sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) by binding to transmembrane helices alone or in association with phospholamban

    Michio Asahi;Yuji Sugita;Kazimierz Kurzydlowski;Stella De Leon

  • Replica-exchange multicanonical and multicanonical replica-exchange Monte Carlo simulations of peptides. I. Formulation and benchmark test

    Ayori Mitsutake;Yuji Sugita;Yuji Sugita;Yuji Sugita;Yuko Okamoto;Yuko Okamoto

  • Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    Takaharu Mori;Naoyuki Miyashita;Wonpil Im;Michael Feig

  • Structural basis of ion pumping by Ca2+-ATPase of sarcoplasmic reticulum

    Chikashi Toyoshima;Hiromi Nomura;Yuji Sugita

Frequent Co-Authors

Michael Feig
Michael Feig Michigan State University
Hirohisa Saito
Hirohisa Saito Juntendo University
Osamu Nureki
Osamu Nureki University of Tokyo
Ryuichiro Ishitani
Ryuichiro Ishitani University of Tokyo
Chikashi Toyoshima
Chikashi Toyoshima University of Tokyo
Yoshiki Yamaguchi
Yoshiki Yamaguchi Tohoku Medical and Pharmaceutical University
Daisuke Kohda
Daisuke Kohda Kyushu University
Masahiro Kinoshita
Masahiro Kinoshita Kyoto University
Toshihide Kobayashi
Toshihide Kobayashi University of Strasbourg
Gozoh Tsujimoto
Gozoh Tsujimoto Kyoto University

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