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Biomolecular Simulations and Data Analysis Lab



DESCRIPTION OF LAB RESEARCH WORK
  • MD simulation method and data analysis method development.
  • Peptide, protein folding, unfolding study, specially aimed at folding, misfolding mechanism which could lead to amyloid fibril.
  • DNA dynamics, DNA –protein, DNA-counterions interaction study.
  • RNA dynamics and folding study.
  • Close collaborations with several experimental groups to explore the underlying mechanism on the molecular, atomic level.
  • Machine learning based drug discovery.


LAB MEMBERS
LEAD PI
Mu Yuguang
Associate Professor

Email: ygmu@ntu.edu.sg
Phone: (65) 6316 2885
Office: SBS-04S-46
Shikhar Saxena
PhD student

Email: shikhar003@e.ntu.edu.sg


CURRENT PROJECTS
  • Understanding off-target effects of CRISPR/Cas9 using molecular dynamics simulations” Mar. 2018- Feb 2021
  • Apply deep learning methods to predict protein-ligand binding affinity.

PUBLICATIONS
Full list of publications can be found here
  • Liu, Yang; Li, Weifeng; Chan-Park, Mary B.; Mu, Yuguang
    ​The Necessity of D-Thr in the New Antibiotic Teixobactin: A Molecular Dynamics Study JOURNAL OF CHEMICAL INFORMATION AND MODELING, Volume: 59 Issue: 4 Pages: 1575-1583, 2019.
  • Awuni, Elvis; Mu, Yuguang
    Effect of A22 on the Conformation of Bacterial Actin MreB INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, Volume: 20 Issue: 6 Article Number: 1304, 2019.
  • Zheng, Liangzhen; Xia, Kelin; Mu, Yuguang
    Ligand Binding Induces Agonistic-Like Conformational Adaptations in Helix 12 of Progesterone Receptor Ligand Binding Domain, FRONTIERS IN CHEMISTRY, Volume: 7, Article Number: 315 (2019)
  • Li, Qing; Li, Xuesong; Ning, Lulu; Tan, Choon-Hong; Mu, Yuguang; Wang, Rong
    Hyperfast Water Transport through Biomimetic Nanochannels from Peptide-Attached (pR)-pillar[5]arene SMALL, Volume: 15 Issue: 6, Article Number: 1804678, 2019.
  • Zheng, Liangzhen; Shi, Jiahai; Mu, Yuguang*
    Dynamics changes of CRISPR-Cas9 systems induced by high fidelity mutations PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Volume: 20 Issue: 43 Pages: 27439-27448, 2018.
  • Liu, Yang; Li, Weifeng; Mu, Yuguang*
    Optimization of replica exchange temperature ladder under the well-tempered ensemble CHEMICAL PHYSICS LETTERS, Volume: 711 Pages: 66-72, 2018.
  • Ning, Lulu; Mu, Yuguang*
    Aggregation of PrP106-126 on surfaces of neutral and negatively charged membranes studied by molecular dynamics simulations, BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, Volume: 1860 Issue: 9 Pages: 1936-1948, 2018.
  • Miao, Yansong; Tipakornsaowapak, Teepiyanut; Zheng, Liangzhen; Mu, Yuguang; Lewellyn, Eric
    Phospho-regulation of intrinsically disordered proteins for actin assembly and endocytosis FEBS JOURNAL, Volume: 285 Issue: 15 Pages: 2762-2784, 2018.
  • Sun, He; Qiao, Zhu; Chua, Khi Pin; Tursic, Alma; Liu, Xu; Gao, Yong-Gui; Mu, Yuguang; Hou, Xingliang; Miao, Yansong,
    Profilin Negatively Regulates Formin-Mediated Actin Assembly to Modulate PAMP-Triggered Plant Immunity CURRENT BIOLOGY,Volume: 28 Issue: 12 Pages: 1882-+, 2018.
  • ​Alhossary, Amr; Awuni, Yaw; Kwoh, Chee Keong; Mu, Yuguang*,
    Proposing drug fragments for dengue virus NS5 protein JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, Volume: 16 Issue: 3, 2018​
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