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Laboratory of Theoretical and Computational Biophysics (Lab TCB)

1. Introduction

Laboratory of Theoretical and Computational Biophysics (Lab TCB) is founded by Ton Duc Thang University in order to investigate the physical insights of biological system behaviors at the atomic and electronic level. The understanding widely apply to resolve numerous interdisciplinary problems involving molecular modeling, drug design, biofuel, material and environment, etc.

2. Mission and vision

The TCB targets to resolve urgency problems in biophysics such as:
- Investigating the conformations of disorder proteins using extensive molecular dynamics simulations.
- Estimating the Gibbs free energy difference of binding between biomolecules.
- Determining the physical insights of metalloproteins such as deoxyhypusine dydroxylase and polysaccharide monooxygenases.
- Discovering tremendous potential inhibitors for Aβ oligomers, neuraminidase, HIV protease, and acetylcholinesterase, etc.

3. Research topics

- Quantum chemical investigations of metalloproteins
- Folding/Misfolding of disorder proteins
- Free energy calculations
- Synthetic materials

4. Current members



Dr. Son Tung Ngo


• Head of Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University

Areas of expertise: Physical Chemistry, Computer-Aided Drug Design, Molecular Modeling, Protein Folding


• Review Editor:
- Frontiers in Chemistry (Impact factor: 4.2)
- Frontiers in Physics (Impact factor: 1.9)

• Associate Editor:
- Current Proteomics

Research track record (until March of 2021):
• ISI papers: 57
• Total ISI Citations: 778
• ISI H-index: 17
• At most 5 top journals:

- Chemical Reviews (Impact factor: 52.7)
- Coordination Chemistry Reviews (Impact factor: 15.4)
- Journal of Biological Chemistry (Impact factor: 4.1)
- Journal of Chemical Information and Modeling (Impact factor: 4.5)
- Journal of Physical Chemistry B (Impact factor: 2.9)


Dr. Nguyen Trung Hai


• Member of Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University

Areas of expertise: Molecular dynamics simulations, free energy calculations, Bayesian data analysis

Research track record (until March of 2021):

• ISI papers: 26
• Total ISI Citations: 253
• ISI H-index: 9
• At most 5 top journals:

- Proceedings of the National Academy of Sciences of the United States of America (Impact factor: 9.5)
- Journal of Chemical Theory and Computation (Impact factor: 5.4) 
- Chemistry-A European Journal (Impact factor: 5.2)
- Dalton transactions (Impact factor 4.1)
- Scientific Reports (Impact factor 4.1)

5. Publications (ISI or Scopus only)

  1. Phuong Nguyen, Ayyalusamy Ramamoorthy, Bikash Sahoo, Jie Zheng, Peter Faller, John Straub, Laura Domínguez, Joan-Emma Shea, Nikolay Dokholyan, Alfonso De Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesne, Guanghong Wei, Fabio Sterpone, Andrew Doig, Philippe Derreumaux (2021), Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes and Amyotrophic Lateral Sclerosis; Chemical Reviews (ISI).
  2. Son Tung Ngo, Nguyen Minh Tam, Minh Quan Pham, and Trung Hai Nguyen (2021); Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro; Journal of Chemical Information and Modeling (ISI).
  3. Son Tung Ngo, Phuong H. Nguyen, and Philippe Derreumaux (2021); Impact of the Rat R5G, Y10F, and H13R Mutations on Tetrameric Aβ42 β-Barrel in a Lipid Bilayer Membrane Model; Journal of Physical Chemistry B (ISI).
  4. Son Tung Ngo, Phuong H. Nguyen and Philippe Derreumaux (2021); Cholesterol Molecules Alter the Energy Landscape of Small Aβ1–42 Oligomers; Journal of Physical Chemistry B (ISI).
  5. Thanh Thuy Tran, Feng Pan, Linh Tran, Christopher Roland and Celeste Sagui (2021); The F19W mutation reduces the binding affinity of the transmembrane Aβ11–40 trimer to the membrane bilayer; RSC Advances (ISI).
  6. Son Tung Ngo, Van Van Vu, Huong Thi Thu Phung (2021); Computational investigation of possible inhibitors of the winged-helix domain of MUS81; Journal of Molecular Graphics and Modelling (ISI).
  7. Minh Q. Dinh, Minh Thuy Le, Son Tung Ngo, Nguyen Thanh Tung (2021); Unifying approach to multilayer metamaterials absorber for bandwidth enhancement; Optics Communications (ISI).
  8. Nguyen Thi Mai, Ngo Thi Lan, Thien Y Vu, Phuong Thi Mai Duong, Nguyen ThanhTung, Huong Thi Thu Phung (2021); Corrigendum to ‘Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations’; Journal of Molecular Graphics and Modelling (ISI).
  9. Son Tung Ngo*, Ngoc Quynh Anh Pham, Ly Thi Le, Duc-Hung Pham*, and Van V. Vu* (2020); Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease; Journal of Chemical Information and Modeling  (ISI).
  10. Minh Quan Pham, Khanh B. Vu, T. Ngoc Han Pham, Le Thi Thuy Huong, Linh Hoang Tran, Nguyen Thanh Tung, Van V. Vu, Trung Hai Nguyen and Son Tung Ngo(2020); Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations; RSC Advances (ISI).
  11. Nguyen Thi Mai, Ngo Thi Lan, Thien Y Vu, Phuong Thi Mai Duong, Nguyen Thanh Tung, Huong Thi Thu Phung (2020); Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations; Journal of Molecular Graphics and Modelling (ISI).
  12. Nguyen Trong Dan, Hoang Duc Quang, Vuong Van Truong, Do Huu Nghi, Nguyen Manh Cuong, To Dao Cuong, Tran Quoc Toan, Long Giang Bach, Nguyen Huu Thuan Anh, Nguyen Thi Mai, Ngo Thi Lan, Luu Van Chinh & Pham Minh Quan (2020); Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3β of new indirubin-3ʹ-oxime derivatives; Scientific Reports (ISI).
  13. Sheeana Gangadoo, Stephanie Owen, Piumie Rajapaksha, Katie Plaisted, Samuel Cheeseman, Hajar Haddara, Vi Khanh Truong, Son Tung Ngo, Van V.Vu, Daniel Cozzolino, Aaron Elbourne, Russell Crawford, Kay Latham, James Chapman(2020); Nano-plastics and their analytical characterisation and fate in the marine environment: From source to sea; Science of The Total Environment (ISI).
  14. Nguyen Thi Mai, Son Tung Ngo, Peter Lievens, Ewald Janssens*, and Nguyen Thanh Tung* (2020); Photofragmentation Patterns of Cobalt Oxide Cations ConOm+ (n = 5–9, m = 4–13): From Oxygen-Deficient to Oxygen-Rich Species; ACS Publications (ISI).
  15. Khanh B.Vu, Truong Le Phuc Nhi, Van V.Vu, SonTung Ngo (2020); How do magnetic, structural, and electronic criteria of aromaticity relate to HOMO – LUMO gap? An evaluation for graphene quantum dot and its derivatives; Chemical Physics (ISI).
  16. Son Tung Ngo (2020); Estimating the ligand‐binding affinity via λ‐dependent umbrella sampling simulations; Journal of Computational Chemistry (ISI).
  17. Son Tung Ngo, Hung Minh Nguyen, Le Thi Thuy Huong, Pham Minh Quan, Vi Khanh Truong, Nguyen Thanh Tung and Van V. Vu (2020); Assessing potential inhibitors of SARS-CoV-2 main protease from available drugs using free energy perturbation simulations; RSC Advances (ISI).
  18. D. C. Nguyen, Thanh Khoa Phung, Dai-Viet N. Vo, Tu Hai Le,Dinh Quang Khieu and Thong Le Minh Pham (2020); Unraveling the effect of Al doping on CO adsorption at ZnO(10[1 with combining macron]0); RSC Advances (ISI).
  19. Ngo Xuan Hoang, Van-Hai Hoang, Thi-Thu-Trang Luu, Hung N. Luu, Thien Ngo, Duong Van Hieu, Nguyen Huu Long, Le Viet Anh, Son Tung Ngo, Yen Thi Kim Nguyen, Byung Woo Han, Thanh Xuan Nguyen, Dinh Thi Thanh Hai, Tran Thi Thu Hien and Phuong-Thao Tran (2020); Design, synthesis and bioevaluation of novel 6-substituted aminoindazole derivatives as anticancer agents; RSC Advances (ISI).
  20. Nguyen, Luong V.; Thu, Nguyen T. (2020); Fixed point results for intuitionistic fuzzy mappings and an application; IOS Press journal (ISI).
  21. Luong V. Nguyen; Nguyen T. Thu (2020); Fréchet Analysis and Sensitivity Relations for the Optimal Time Problem; IEEE Access (ISI).
  22. Huynh Minh Hung, Minh Tho Nguyen, Phuong-Thao Tran, Vi Khanh Truong, James Chapman, Le Huu Quynh Anh, , Philippe Derreumaux, Van V. Vu and Son Tung Ngo* (2020); Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide; Journal of Chemical Information and Modeling (ISI).
  23. Son Tung Ngo*, Han N. Phan, Chinh N. Le, Nhung C. T. Ngo, Khanh Bao Vu, Nguyen Thanh Tung, Cuong X. Luu* and Van V. Vu* (2020); Fine Tuning of the Copper Active Site in Polysaccharide Monooxygenases; The Journal of Physical Chemistry B (ISI).
  24. Son Tung Ngo, Nam Dao Hong, Le Huu Quynh Anh, Dinh Minh Hiep and Nguyen Thanh Tung (2020); Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach; RSC Advances (ISI).
  25. Nguyen Thanh Nguyen, Trung Hai Nguyen, T. Ngoc Han Pham, Nguyen Truong Huy, Mai Van Bay, Minh Quan Pham , Pham Cam Nam, Van V. Vu and Son Tung Ngo* (2020); Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity; ACS Publications (ISI).
  26. Son Tung Ngo , Trung Hai Nguyen , Nguyen Thanh Tung , Pham Cam Nam , Khanh B. Vu , Van V. Vu (2019); Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy; Computational Chemistry (ISI).
  27. Trung Hai Nguyen, Van Ngo, João Paulo Castro Zerba, Sergei Noskov, and David D. L. Minh (2019); Nonequilibrium path-ensemble averages for symmetric protocols; The Journal of Chemical Physics (ISI).
  28. Van-Hai Hoang, Van T. H. Ngo, Minghua Cui, Nguyen Van Manh, Phuong-Thao Tran, Jihyae Ann, Hee-Jin Ha, Hee Kim, Kwanghyun Choi, Young-Ho Kim, Hyerim Chang, Stephani Joy Y. Macalino, Jiyoun Lee, Sun Choi* and Jeewoo Lee* (2019); Discovery of Conformationally Restricted Human Glutaminyl Cyclase Inhibitors as Potent Anti-Alzheimer’s Agents by Structure-Based Design; Journal of Medicinal Chemistry (ISI).
  29. Phuong-Thao Tran, Van-Hai Hoang, Jeewoo Lee, Tran Thi Thu Hien, Nguyen Thanh Tung and Son Tung Ngo* (2019); In vitro and in silico determination of glutaminyl cyclase inhibitors; RSC Advances (ISI).
  30. Nguyen Thanh Tung, Philippe Derreumaux, Van V. Vu, Pham Cam Nam, and Son Tung Ngo* (2019); C-Terminal Plays as the Possible Nucleation of the Self-Aggregation of the S-Shape Aβ11–42 Tetramer in Solution: Intensive MD Study; ACS Omega (ISI).
  31. Van V. Vu, John A. Hangasky, Tyler C. Detomasi, Skylar J. W. Henry, Son Tung Ngo**, Elise A. Span and Michael A. Marletta (2019); Substrate selectivity in starch polysaccharide monooxygenases; Journal of Biological Chemistry (ISI).
  32. Ngo Thi Lan, Khanh B. Vu, Minh Khue Dao Ngoc, Phuong-Thao Tran, Dinh Minh Hiep, Nguyen Thanh Tung, Son Tung Ngo (2019); Prediction of AChE-ligand affinity using the umbrella sampling simulation; Journal of Molecular Graphics and Modelling(ISI).
  33. Son Tung Ngo*, Phuong Duy Tran-Le, Giap T. Ho, Loan Q. Le, Le Minh Bui, Bao Khanh Vu, Huong Thi Thu Phung , Hoang-Dung Nguyen, Thanh-Sang Vo and Van V. Vu (2019); Interaction of carbohydrate binding module 20 with starch substrates; RSC Advances (ISI).
  34. Son Tung Ngo, Binh Khanh Mai, Philippe Derreumaux and Van V. Vu (2019); Adequate prediction for inhibitor affinity of Aβ40 protofibril using the linear interaction energy method ; RSC Advances (ISI).
  35. Khanh B.Vu, Long Giang Bach, Thuan Van Tran, Nguyen Thi Thuong, Ha N.Giang, Quynh Thi Phuong Bui, Son Tung Ngo (2019); Gold@silica catalyst: Porosity of silica shells switches catalytic reactions ; Chemical Physics Letters (ISI).
  36. Tran Van Huynh, Bui Son Tung, Bui Xuan Khuyen, Son Tung Ngo, Vu Dinh Lam, Nguyen Thanh Tung (2019); Controlling the absorption strength in bidirectional terahertz metamaterial absorbers with patterned graphene ; Computational Materials Science (ISI).
  37. Nguyen, Luong V.;Hoc, Nguyen H. (2019); On nonlinear F-contractive fuzzy mappings ; IOS Press journal (ISI).
  38. Son Tung Ngo, Philippe Derreumaux, Van V. Vu (2019); Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions; Journal Of Physical Chemistry B (ISI).
  39. Son Tung Ngo, Khanh B. Vu, Le Minh Bui, and Van V. Vu; Effective Estimation of Ligand Binding Affinity using Biased Sampling Method; ACS Omega (ISI).
  40. Son Tung Ngo, Huong Phung Thi Thu, Khanh B. Vu, Van V. Vu (2018); Atomistic Investigation of an Iowa Amyloid-β Trimer in Aqueous Solution; RSC Advances (ISI). 
  41. Bao Khanh Vu, Van V. Vu, Huong Phung Thi Thu, Ha N. Giang, Nguyen Minh Tam, Son Tung Ngo (2018); Conjugated polymers: A systematic investigation of their electronic and geometric properties using density functional theory and semi-empirical methods; Synthetic Metals (ISI).

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