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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-Ngo-Son-Tung-DEMASTED.jpg

 

Dr. Son Tung Ngo

Positions:

• 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

Editorship:

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

• Associate Editor:
- Current Proteomics

Research track record (until Aug of 2019):
• ISI papers: 48
• Total ISI Citations: 646
• ISI H-index: 14
• At most 5 top journals:
- 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)
- Journal of Computational Chemistry (Impact factor: 3.0)

Nguyen_Trung_Hai.png

Dr. Nguyen Trung Hai

Positions:

• 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 2019):

• ISI papers: 21
• Total ISI Citations: 208
• ISI H-index: 8
• 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)

DEMASTED_Nguyen_Van_Luong.jpg

Dr. Nguyen Van Luong

Positions:

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

Areas of expertise: Optimal control theory, nonsmooth analysis, optimization, fixed point theory and applications

Dr. Ngo Thi Hong Van

Dr. Ngo Thi Hong Van

Positions:

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

Areas of expertise: Drug design

COMCHEM_Tran_Thi_Thuy_Linh.jpg

Dr. Tran Thi Thuy Linh

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

Areas of expertise: Computer Aided Drug Design, Molecular Modeling

Dr-Tran-Thanh-Thuy.jpg

Dr. Tran Thanh Thuy

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

Areas of expertise: Molecular dynamics simulations, coarse-grained modeling, disorder protein prediction

 

Dr. Nguyen Dinh Chuong

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

Areas of expertise: 

COMCHEM_Nguyen_Thi_Mai.JPG

Msc. Nguyen Thi Mai

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

Areas of expertise: Computational chemistry

5. Publications (ISI or Scopus only)

  1. Nguyen, Luong V.; Thu, Nguyen T. (2020); Fixed point results for intuitionistic fuzzy mappings and an application; IOS Press journal (ISI).
  2. Luong V. Nguyen; Nguyen T. Thu (2020); Fréchet Analysis and Sensitivity Relations for the Optimal Time Problem; IEEE Access (ISI).
  3. 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).
  4. 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).
  5. 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).
  6. 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; (ISI).
  7. 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).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. Nguyen, Luong V.;Hoc, Nguyen H. (2019); On nonlinear F-contractive fuzzy mappings ; IOS Press journal (ISI).
  19. 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).
  20. 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).
  21. 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). 
  22. 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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