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Pham Dang Lan; Daniel Allen Nissley; Ian Sitarik; Quyen V. Vu; Yang Jiang; Philip To; Yingzi Xia; Stephen D. Fried; Mai Suan Li; Edward P. OBrien - Synonymous mutations can alter protein dimerization through localized interface misfolding involving self-entanglements - Journal of Molecular Biology - Link - PDF |
2024 |
SCI |
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Pham Dang Lan; Daniel A. Nissley; Edward P. O’Brien; Toan T. Nguyen; Mai Suan Li - Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2 - The Journal of Chemical Physics - Link - PDF |
2024 |
Other |
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Thanh Q. Bui, Ton That Huu Dat, Phan Tu Quy, Nguyen Thi Thanh Hai, Nguyen Minh Thai, Nguyen Vinh Phu, Le Van Tuan, Lam K. Huynh, Mai Suan Li & Nguyen Thi Ai Nhung - Identification of potential anti-hyperglycemic compounds in Cordyceps militaris ethyl acetate extract: in vitro and in silico studies - Journal of Biomolecular Structure and Dynamics - Link - PDF |
2023 |
SCI |
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Hung Nguyen, Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Mateusz Sikora and Mai Suan Li - Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation - Chemical Society Reviews - Link - PDF |
2023 |
SCI |
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Pawel Krupa, Giovanni La Penna, and Mai Suan Li - Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role - International Journal of Molecular Sciences - Link - PDF |
2023 |
SCI |
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Ritaban Halder, Daniel A. Nissley, Ian Sitarik, Yang Jiang, Yiyun Rao, Quyen V. Vu, Mai Suan Li, Justin Pritchard & Edward P. O’Brien - How soluble misfolded proteins bypass chaperones at the molecular level - nature communications - Link - PDF |
2023 |
SCI |
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Quyen V. Vu, Daniel A. Nissley, Yang Jiang, Edward P. O’Brien, and Mai Suan Li - Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study - The Journal of Physical Chemistry B - Link - PDF |
2023 |
SCI |
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Ankur Gupta, Pawel Krupa, Oskar Engberg, Magdalena Krupa, Ankur Chaudhary, Mai Suan Li, Daniel Huster, and Sudipta Maiti - Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations - The Journal of Physical Chemistry B - Link - PDF |
2023 |
SCI |
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Nguyen Hoang Linh, Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux, Thi Ly Mai, and Phuong H. Nguyen - Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse - The Journal of Chemical Physics - Link - PDF |
2022 |
SCI |
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Hoang Linh Nguyen, Nguyen Quoc Thai & Mai Suan Li - Identifying inhibitors of NSP16-NSP10 of SARS- CoV-2 from large databases - Journal of Biomolecular Structure and Dynamics - Link - PDF |
2022 |
SCI |
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Tran Thi Minh Thu and Mai Suan Li - Protein aggregation rate depends on mechanical stability of fibrillar structure - The Journal of Chemical Physics - Link - PDF |
2022 |
SCI |
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Hoang Linh Nguyen, Nguyen Quoc Thai, Phuong H. Nguyen, and Mai Suan Li - SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation - The Journal of Physical Chemistry B - Link - PDF |
2022 |
SCI |
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Hung Nguyen, Mai Suan Li - Antibody–nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants - Scientific Reports - Link - PDF |
2022 |
SCI |
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Hoang Linh Nguyen, Huynh Quang Linh, Pawel Krupa, Giovanni La Penna, and Mai Suan Li - Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity - The Journal of Physical Chemistry B - Link - PDF |
2022 |
SCI |
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Hoang Linh Nguyen, Nguyen Quoc Thai, and Mai Suan Li - Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution - Journal of Chemical Theory and Computation - Link - PDF |
2022 |
SCI |
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Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, and Mai Suan Li - Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability - The Journal of Physical Chemistry B - Link - PDF |
2022 |
SCI |
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Nguyen Truong Co, Mai Suan Li, Pawel Krupa - Computational Models for the Study of Protein Aggregation - Computer Simulations of Aggregation of Proteins and Peptides - Link - PDF |
2022 |
Book |
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Hoang Linh Nguyen, Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang and Phuong H. Nguyen - Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations - Physical Chemistry Chemical Physics - Link - PDF |
2022 |
SCI |
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Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch, and Edward P. O’Brien* - Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force - Biochemistry - Link - PDF |
2021 |
SCI |
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Quyen V. Vu, Yang Jiang, Mai Suan Li and Edward P. O'Brien - The driving force for co-translational protein folding is weaker in the ribosome vestibule due to greater water ordering - Chemical Science - Link - PDF |
2021 |
SCI |
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Hong An Pham, Duc Toan Truong, and Mai Suan Li - Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding - Journal of physical chemistry B - Link - PDF |
2021 |
SCI |
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Adolfo B. Poma, Tran Thi Minh Thu, Lam Tang Minh Tri, Hoang Linh Nguyen, and Mai Suan Li - Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations - Journal of physical chemistry B - Link - PDF |
2021 |
SCI |
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Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, and Phuong H. Nguyen - Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study - Langmuir - Link - PDF |
2021 |
SCI |
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Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, and Mai Suan Li - Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody - Journal of physical chemistry B - Link - PDF |
2021 |
SCI |
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Nguyen Truong Co and Mai Suan Li - Effect of Surface Roughness on Aggregation of Polypeptide Chains: A Monte Carlo Study - biomolecules - Link - PDF |
2021 |
SCI |
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Phuong H. Nguyen, Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Dominguez, Joan-Emma Shea, Nikolay V. 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 Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, and Philippe Derreumaux - Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis - ACS Chemical Reviews - Link - PDF |
2021 |
SCI |
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Martina Banchelli, Roberta Cascella, Cristiano D’Andrea, Giovanni La Penna*, Mai Suan Li, Fabrizio Machetti, Paolo Matteini, and Silvia Pizzanelli - Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling - ACS Chemical Neuroscience - Link - PDF |
2021 |
SCI |
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Hoang Linh Nguyen, Nguyen Quoc Thai, Duc Toan Truong, and Mai Suan Li - Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations - Journal of physical chemistry B - Link - PDF |
2020 |
SCI |
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Daniela Marasco, Caterina Vicidomini, Pawel Krupa, Federica Cioffi, Pham Dinh Quoc Huy, Mai Suan Li, Daniele Florio, Kerensa Broersen, Maria Francesca De Pandis, and Giovanni N.Roviello - Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine based compounds on β-amyloid aggregation - Chemico-Biological Interactions - Link - PDF |
2021 |
SCI |
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Hoang Linh Nguyen, Huynh Quang Linh, Paolo Matteini, Giovanni La Penna, and Mai Suan Li - Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study - Journal of physical chemistry B - Link - PDF |
2020 |
SCI |
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Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Daniel A. Nissley, Edward P. O'Brien, and Mai Suan Li - Does SARS-CoV-2 Bind to Human ACE2 Stronger Than SARS-CoV? - The journal of physical chemistry B - Link - PDF |
2020 |
SCI |
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Tri Pham, Hoang Linh Nguyen, Tuyn Phan-Toai, Hung Nguyen - Investigation of Binding Affinity between Potential Antiviral Agents and PB2 Protein of Influenza A: Non-equilibrium Molecular Dynamics Simulation Approach - International journal of medical sciences - Link - PDF |
2020 |
SCI |
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Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, Toan T Nguyen, Shikha Nangia, and Phuong H. Nguyen - Molecular mechanism of ultrasound interaction with a blood brain barrier mode - The Journal of Chemical Physics - Link - PDF |
2020 |
SCI |
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Subramanian Boopathi, Pham Dinh Quoc Huy, Wendy Gonzalez, Panagiotis E. Theodorakis, Mai Suan Li - Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies - Proteins - Link - PDF |
2020 |
SCI |
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Martina Banchelli, Roberta Cascella, Cristiano D'Andrea, Leszek Cabaj, Iacopo Osticioli, Daniele Ciofini, Mai Suan Li, Krzysztof Skupien, Marella de Angelis, Salvatore Siano, Cristina Cecchi, Roberto Pini, Giovanni La Penna, Fabrizio Chiti and Paolo Matteini - Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers - RSC Advances - Link - PDF |
2020 |
SCI |
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Nguyen Quoc Thai, Panagiotis E. Theodorakis, and Mai Suan Li - Fast Estimation of the Blood–Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane - Journal of Chemical Information and Modeling - Link - PDF |
2020 |
SCI |
|
Kiet Ho, Duc Toan Truong, and Mai Suan Li - How Good is Jarzynski’s Equality for Computer-Aided Drug Design? - The journal of physical chemistry B - Link - PDF |
2020 |
SCI |
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Dinh Quoc Huy Pham, Pawel Krupa, Hoang Linh Nguyen, Giovanni La Penna, Mai Suan Li* - Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane - The journal of Physical Chemistry B - Link - PDF |
2020 |
SCI |
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Daniel A. Nissley, Quyen V. Vu, Fabio Trovato, Nabeel Ahmed, Yang Jiang, Mai Suan Li, Edward P. O’Brien - Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling - Journal of the American Chemical Society - Link - PDF |
2020 |
SCI |
|
Nguyen Truong Co, Pham Dang Lan, Pham Dinh Quoc Huy, and Mai Suan Li - Heat-induced degradation of fibrils: Exponential vs logistic kinetics - The Journal of Chemical Physics - Link - PDF |
2020 |
SCI |
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Miroslav Gancar, Kiet Ho, Sk. Abdul Mohid, Nguyen Quoc Thai, Zuzana Bednarikova, H. Linh Nguyen, Anirban Bhunia, Eugenie Nepovimova, Mai Suan Li, and Zuzana Gazova - 7-Methoxytacrine and 2-Aminobenzothiazole Heterodimers: Structure–Mechanism Relationship of Amyloid Inhibitors Based on Rational Design - ACS Chemical Neuroscience - Link - PDF |
2020 |
SCI |
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Hoang Linh Nguyen, Pawel Krupa, Nguyen Minh Hai, Huynh Quang Linh, Mai Suan Li - Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations - The Journal of Physical Chemistry B - Link - PDF |
2019 |
SCI |
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Pawel Krupa , Pham Dinh Quoc Huy, and Mai Suan Li - Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components - The Journal of Chemical Physics - Link - PDF |
2019 |
SCI |
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Tran Thi Minh Thu, Shu-Hsiang Huang, Ly Anh Tu, Shang-Ting Fang, Mai Suan Li, Yi-Cheng Chen - G37V mutation of Aβ42 induces a nontoxic ellipse-like aggregate: An in vitro and in silico study - Neurochemistry International - Link - PDF |
2019 |
SCI |
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Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux, and Phuong H. Nguyen - Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion - The Journal of Chemical Physics - Link - PDF |
2019 |
SCI |
|
Giovanni La Penna, and Mai Suan Li - Computational models explain how copper binding to amyloid-β peptide oligomers enhances oxidative pathways - Physical Chemistry Chemical Physics - Link - PDF |
2019 |
SCI |
|
Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux, and Phuong H. Nguyen - Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level - The Journal of Chemical Physics - Link - PDF |
2019 |
SCI |
|
Tran Thi Minh Thu, Nguyen Truong Co, Ly Anh Tu, and Mai Suan Li - Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state - The Journal of Chemical Physics - Link - PDF |
2019 |
SCI |
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Hoang Linh Nguyen, Pham Hong An, Nguyen Quoc Thai, Huynh Quang Linh, Mai Suan Li - Erythromycin, Cethromycin and Solithromycin display similar binding affinities to the E. coli's ribosome: A molecular simulation study - Journal of Molecular Graphics and Modelling - Link - PDF |
2019 |
SCI |
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Viet Hoang Man, Phan Minh Truong, Mai Suan Li, Junmei Wang, Nguyen-Thi Van-Oanh, Philippe Derreumaux , and Phuong H. Nguyen - Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation - The Journal of Physical Chemistry B - Link - PDF |
2019 |
SCI |
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Adolfo B. Poma, Horacio V. Guzman, Mai Suan Li and Panagiotis E. Theodorakis - Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies - Beilstein Journal of Nanotechnology - Link - PDF |
2019 |
SCI |
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Pham Dang Lan, Maksim Kouza, Andrzej Kloczkowski, and Mai Suan Li - A topological order parameter for describing folding free energy landscapes of proteins - The Journal of Chemical Physics 149, 175101 - Link - PDF |
2018 |
SCI |
|
Huy Dinh Quoc Pham, Nguyen Quoc Thai, Zuzana Bednarikova, Huynh Quang Linh, Zuzana Gazova and Mai Suan Li - Bexarotene cannot reduce amyloid beta plaques through inhibition of production of amyloid beta peptides: in silico and in vitro study - Physical Chemistry Chemical Physics - Link - PDF |
2018 |
SCI |
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Dinh Quoc Huy Pham, Mai Suan Li, and Giovanni La Penna - Copper Binding Induces Polymorphism in Amyloid-β Peptide: Results of Computational Models - Journal of Physical Chemistry B, 122 (29), 7243–7252 (2018) - Link - PDF |
2018 |
SCI |
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Nguyen Quoc Thai, Zuzana Bednarikova, Miroslav Gancar, Huynh Quang Linh, Chin-Kun Hu, Mai Suan Li, and Zuzana Gazova - Compound CID 9998128 Is a Potential Multitarget Drug for Alzheimer’s Disease - ACS Chemical Neuroscience - Link - PDF |
2018 |
SCI |
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Maksim Kouza, Nguyen Truong Co, Mai Suan Li, Sebastian Kmiecik, Andrzej Kolinski, Andrzej Kloczkowski, and Irina Alexandra Buhimschi - Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study - The Journal of Chemical Physics - Link - PDF |
2018 |
SCI |
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Hung Nguyen, Tri Pham, Hoang Linh Nguyen, Tuyn Phan - Investigation of Binding Affinity Between Prokaryotic Proteins (AHU-IHF) and DNAs: Steered Molecular Dynamics Approach - Applied Biochemistry and Biotechnology - Link - PDF |
2018 |
SCI |
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Hoang Linh Nguyen, Dang Lan Pham, Edward P. O’Brien & Mai Suan Li - Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins - Scientific Reports, volume 8, Article number: 6460 - Link - PDF |
2018 |
SCI |
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Duc Toan Truong and Mai Suan Li - Probing the Binding Affinity by Jarzynski’s Nonequilibrium Binding Free Energy and Rupture Time - Journal of Physical Chemistry B, DOI: 10.1021/acs.jpcb.8b02137 - Link - PDF |
2018 |
SCI |
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Giovanni La Penna and Mai Suan Li - Towards High‐Throughput Modelling of Copper Reactivity Induced by Structural Disorder in Amyloid Peptides - Chemistry: A European Journal; 2018, 24, 1 – 13 - Link - PDF |
2018 |
SCI |
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Michał Wojciechowski, Bartosz Różycki, Pham Dinh Quoc Huy, Mai Suan Li, Edward A. Bayer & Marek Cieplak - Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module - Scientific Reports, 8:5051 (2018) - Link - PDF |
2018 |
SCI |
|
Hung Nguyen, Ly Le - Investigation of changes in structure and thermodynamics of Spruce Budworm antifreeze protein under subfreezing temperature - Scientific Reports. 7:40032 - Link - PDF |
2017 |
SCI |
|
Hung Nguyen, Thu Nguyen, Ly Le - Computational study of Glucose 6 phosphate dehydrogenase deficiencies using molecular dynamics simulation - South Asian Journal of Life Sciences. 4(1):32-39 - Link - PDF |
2016 |
Other |
|
Hung Nguyen, Thanh Dac Van, Nhut Tran, Ly Le - Exploring the effects of subfreezing temperature and salt concentration on ice growth inhibition of Antarctic Gram-negative bacterium Marinomonas Primoryensis using coarse grained simulation - Applied Biochemistry and Biotechnology. 178(8):1534-1545 - Link - PDF |
2016 |
SCI |
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Hung Nguyen, Hieu Thanh Nguyen, Ly Thi Le - Investigation of free energy profiles of amantadine and rimantadine in the AM2 binding pocket - European Biophysics Journal. 45(1):63-70 - Link - PDF |
2015 |
SCI |
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Hung Nguyen, Thanh Dac Van, Ly Le - Coarse grained simulation reveals antifreeze properties of hyperactive antifreeze protein from Antarctic bacterium Colwellia sp - Chemical Physics Letters. 638:137-143. - Link - PDF |
2015 |
SCI |
|
Hung Nguyen, Tien Tran, Yoshifumi Fukunishi, Junichi Higo, Haruki Nakamura, Ly Le - Computational study of drug binding affinity to Influenza A neuraminidase using smooth reaction path generation (SRPG) method - Journal of Chemical Information and Modelling - Link - PDF |
2015 |
SCI |
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Hung Nguyen, Ly Le - Steered molecular dynamics approach for promising drugs for influenza A virus targeting M2 channel protein - European Biophysics Journal. 44(6):447-455. doi: 10.1007/s00249-015-1047-4 - Link - PDF |
2015 |
SCI |
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Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, and Phuong H. Nguyen - Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study - The Journal of Chemical Physics - Link - PDF |
2018 |
SCI |
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Hung Nguyen, Hoang Linh Nguyen, Huynh Quang Linh, Minh Tho Nguyen - Binding affinity of the L-742,001 inhibitor to the endonuclease domain of A/H1N1/PA influenza virus variants: Molecular simulation approaches - Chemical Physics 500 (2018) 26–36 - Link - PDF |
2018 |
SCI |
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Nguyen Quoc Thai, Ngan Quy Nguyen, Chuong Nguyen, Truong Quy Nguyen, Kiet Ho, Trung Tin Nguyen, Mai Suan Li - Screening potential inhibitors for cancer target LSD1 from natural products by steered molecular dynamics - Molecular Simulation - Link - PDF |
2017 |
SCI |
|
Nguyen Quoc Thai, Nguyen Hoang Linh, Huynh Quang Linh, and Mai Suan Li - Protocol for fast screening of multi-target drug candidates: Application to Alzheimer’s disease - Journal of Molecular Graphics and Modelling - Link - PDF |
2017 |
SCI |
|
Hung Nguyen, Nhat Do, Tuyn Phan, Tri Pham - Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B) - Applied Biochemistry and Biotechnology, 1-13 - Link - PDF |
2017 |
SCI |
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Pham Dinh Quoc Huy, Nguyen Quoc Thai, Zuzana Bednarikova, Le Huu Phuc, Huynh Quang Linh, Zuzana Gazova, and Mai Suan Li - Bexarotene does not clear amyloid beta plaques but delays fibril growth: Molecular mechanisms - ACS Chemical Neuroscience - Link - PDF |
2017 |
SCI |
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Nguyen Hoang Linh, Tran Thi Minh Thu, LyAnh Tu, Chin-Kun Hu, and Mai Suan Li - Impact of Mutations at C-Terminus on Structures and Dynamics of Aβ40 and Aβ42: A Molecular Simulation Study - The Journal of Physical Chemistry B - Link - PDF |
2017 |
SCI |
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Maksim Kouza, Pham Dang Lan, A. M. Gabovich, A. Kolinski, and Mai Suan Li - Switch from thermal to force-driven pathways of protein refolding - The Journal of Chemical Physics - Link - PDF |
2017 |
SCI |
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Quan Van Vuong, Pham Dinh Quoc Huy, Giovanni La Penna, Peter Faller, and Mai Suan Li - Impact of Cu(II) binding on Structures and Dynamics of Ab42 Monomer and Dimer: Molecular Dynamics Study - ACS Chem NeuroScience, doi:10.1021/acschemneuro.6b00109 - Link - PDF |
2016 |
SCI-E |
|
Nguyen Quoc Thai, Ning-Hsuan Tseng, Mui Thi Vu, Tin Trung Nguyen, Huynh Quang Linh, Chin-Kun Hu, Yun-Ru Chen, and Mai Suan Li - Discovery of DNA dyes Hoechst 34580 and 33342 as Good Candidates for Inhibiting Amyloid Beta Formation: In silico and in vitro Study - J. Computer-Aided Mol Design, doi:10.1007/s10822-016-9932-1 - Link - PDF |
2016 |
SCI |
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Nguyen Hoang Linh, Tran Thi Minh Thu, Phan Minh Truong, Pham Dang Lan, Man Hoang Viet, Phuong H. Nguyen, T. Ly Anh, Y-C. Chen, and Mai Suan Li - Ab41 Aggregates More Like Ab40 Than Like Ab42: In silico and in vitro Study - J. Phys. Chem B 120 (30), 7371-7379 - Link - PDF |
2016 |
SCI |
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Yu-Jen Chang, Nguyen Hoang Linh, Hui-Ming Yu, Mai Suan Li, and Yun-Ru Chen - Alzheimer's Amyloid-beta Sequesters Caspase-3 via its C-terminal Tail - ACS Chemical Neuroscience 7 (8), 1097-1106 - Link - PDF |
2016 |
SCI-E |
|
Tin Trung Nguyen, Duy Phuoc Tran, Huy Dinh Quoc Pham, Zung Hoang, Paolo Carloni, Phuc Van Pham, Chuong Nguyen, and Mai Suan Li - Ligand binding to anti-cancer target CD44 investigated by molecular simulations - Journal of Molecular Modeling 22 (7), Article Number: 165 - Link - PDF |
2016 |
SCI-E |
|
Z. Bednarikova, PDQ Huy, M.M. Mocanu, D. Fedunova, M.S. Li, and Z. Gazova - Fullerenol C-60(OH)(16) prevents amyloid fibrillization of A beta(40) - in vitro and in silico approach - Phys Chem Chem Phys 18 (28), 18855-18867 - Link - PDF |
2016 |
SCI |
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Son Tung Ngo, Shang-Ting Fang, Shu-Hsiang Huang, Chao-Liang Chou, Pham Dinh Quoc Huy, Mai Suan Li, and Yi-Cheng Chen - Anti-arrhythmic medication Propafenone is potential drug for Alzheimer's disease by inhibiting aggregation of Abeta: in silico and in vitro studies - Journal of Chem Inf Model. 56 (7), 1344-1356 - Link - PDF |
2016 |
SCI |
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Quan Van Vuong, Tin Trung Nguyen, and Mai Suan Li - A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics - J. Chem. Info. Model. 55, 2731-2738 - Link - PDF |
2015 |
SCI |
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M.H. Viet, N.T.V. Oanh, Philippe Derreumaux, Mai Suan Li, Christopher Roland,Celeste Sagui and Phuong H. Nguyen. - Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of virus - Phys. Chem. Chem. Phys 18, 11951-11958 - Link - PDF |
2016 |
SCI-E |
|
Phuc Nguyen, Trang Tran, Thanh Truong and Ly Le - Computational Evaluation of Selectivity of Triazole- and Amide-Based Drug Candidates, Flavanone Derivatives and Synthesized Steroid Compounds for Treatment of Diabetes Type II - Journal of Life Science - Link - PDF |
2012 |
Other |
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Nguyễn Ngọc Đoan Trang và Lê Thị Lý - Review on Targeted Proteins for Diabetes Drug Design - Advances in Natural Sciences: Nanoscience and Nanotechnology - Link - PDF |
2012 |
Other |
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Man Hoang Viet, Phuong H. Nguyen, Son Tung Ngo, Mai Suan Li, and Philippe Derreumaux - Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of Aβ40 and Aβ42 - ACS Chemical Neuroscience - Link - PDF |
2013 |
SCI-E |
|
Hsin-Lin Chiang, Son Tung Ngo, Chun-Jung Chen, Chin-Kun Hu, Mai Suan Li - Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin - PLoS ONE - Link - PDF |
2013 |
SCI-E |
|
Man Hoang Viet, Chun-Yu Chen, Chin-Kun Hu, Yun-Ru Chen, Mai Suan Li - Discovery of Dihydrochalcone as Potential Lead for Alzheimer’s Disease: In Silico and In Vitro Study - PLoS ONE - Link - PDF |
2013 |
SCI-E |
|
Raphael Tze Chuen Lee, Vithiagaran Gunalan, Thanh Dac Van, Ly Thi Le, Frank Eisenhaber and Sebastian Maurer-Stroh - A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus - Biology Direct - Link - PDF |
2013 |
SCI-E |
|
Quy Trinh, Ly Le - An Investigation of Antidiabetic activities of Bioactive compounds in Euphorbia Hirta linn using Molecular Docking and Pharmacophore - Medicinal Chemistry Research - Link - PDF |
2013 |
SCI-E |
|
Nhut Tran, Linh Tran, Ly Le - Strategy in structure-based drug design for influenza A virus targeting M2 channel proteins - Medicinal chemistry research - Link - PDF |
2013 |
SCI-E |
|
Trang Truc Nguyen, Man Hoang Viet, and Mai Suan Li - Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase - The Scientific World Journal - Link - PDF |
2014 |
SCI-E |
|
Linh Tran & Ly Le - Recent Progress and Challenges in Computer-aided Design of Inhibitors for Influenza A M2 Channel Proteins - Medicinal Chemistry Research - Link - PDF |
2014 |
SCI-E |
|
Tăng Thị Ngọc Nữ và Lê Thị Lý - Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family - Evolutionary Bioinformatics - Link - PDF |
2014 |
SCI-E |
|
Quan Van Vuong, Zuzana Bednarikova, Andrea Antosova, Pham Dinh Quoc Huy, Katarina Siposova, Nguyen Anh Tuan, Mai Suan Li and Zuzana Gazova - Inhibition of insulin amyloid fibrillization by glyco-acridines: an in vitro and in silico study - Med. Chem. Commun - Link - PDF |
2015 |
SCI-E |
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Lawrence M. Pratt, Stewart Voit, Binh Khanh Mai and Bich Lien H. Nguyen - Lithium Cuprate Coupling Reactions: Evaluation of Computational Methods for Determination of the Reaction Mechanisms - The Journal of Physical Chemistry A - Link - PDF |
2010 |
SCI-E |
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Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong and Klaus Schulten - Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases - PLoS Computational Biology - Link - PDF |
2010 |
SCI-E |
|
Gali Arad-Haase, Silvia G. Chuartzman, Shlomi Dagan, Reinat Nevo, Maksim Kouza, Binh Khanh Mai, Hung Tien Nguyen, Mai Suan Li and Ziv Reich - Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations - Biophysical Journal - Link - PDF |
2010 |
SCI-E |
|
Hoang Bao Nam, Maksim Kouza, Hoang Zung, and Mai Suan Li - Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations - The Journal of Chemical Physics - Link - PDF |
2010 |
SCI-E |
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Mai Suan Li, Nguyen Truong Co, G. Reddy, C-K Hu and D. Thirumalai - Factors governing fibrillogenesis of polypeptide chains revealed by lattice models - Physical Review Letters - Link - PDF |
2010 |
SCI-E |
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Binh Khanh Mai, Man Hoang Viet, and Mai Suan Li - Top-Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach - Journal of Chemical Information and Modeling - Link - PDF |
2010 |
SCI-E |
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Man Hoang Viet, Son Tung Ngo, Nguyen Sy Lam and Mai Suan Li - Inhibition of aggregation of amyloid peptides by beta-sheet breaker peptides and their binding affinity - The Journal of Physical Chemistry B - Link - PDF |
2011 |
SCI-E |
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Binh Khanh Mai and Mai Suan Li - Neuraminidase Inhibitor R-125489 - A Promising Drug for Treating Influenza Virus: Steered Molecular Dynamics Approach - Biochemical and Biophysical Research Communications - Link - PDF |
2011 |
SCI-E |
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Trang Truc Nguyen, Binh Khanh Mai and Mai Suan Li - Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields - Journal of Chemical Information and Modeling - Link - PDF |
2011 |
SCI-E |
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Mai Suan Li and Binh Khanh Mai - Steered molecular dynamics - a promising tool for drug design - Current Bioinformatics - Link - PDF |
2012 |
SCI |
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Ngô Sơn Tùng và Mai Xuân Lý - Curcumin binds to AB1-40 peptides and fibrils stronger than ibuprofen and naproxen - The Journal of Physical Chemistry B - Link - PDF |
2012 |
SCI-E |
|
Nguyễn Trường Cơ và Mai Xuân Lý - New method for determining size of critical nucleus - The journal of Chemical Physics - Link - PDF |
2012 |
SCI |
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Ngoc-Tram Hoang-Do, Dang-Lan Pham, Van-Hoang Le - Exact numerical solutions of the Schrödinger equation for a two-dimensional exciton in a constant magneticfield of arbitrary strength - Physical B: Condensed Matter - Link - PDF |
2013 |
SCI-E |
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Trang Tran, Ly Le, Thanh Truong - Discover Binding Pathways Using the sliding grid-box docking approach: Application to Binding Pathways of Oseltamivir to avian influenza H5N1 neuraminidase - Journal of Computer Aided Molecular Design - Link - PDF |
2013 |
SCI |
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Nguyen Truong Co, Chin-Kun Hu and Mai Suan Li - Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models - The Journal of Chemical Physics - Link - PDF |
2013 |
SCI-E |
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Pham Dinh Quoc Huy, Yao-Chung Yu, Son Tung Ngo, Tran Van Thao, Chin-piao Chen, Mai Suan Li, Yi-Cheng Chen - In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease - BBA-General Subjects - Link - PDF |
2013 |
Other |
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Quan Van Vuong, Katarina Siposova, Trang Truc Nguyen, Andrea Antosova, Lucia Balogova, Ladislav Drajna, Jan Imrich, Mai Suan Li and Zuzana Gazova - Binding of Glyco-acridine Derivatives to Lysozyme leads to Inhibition of Amyloid Fibrillization - Biomacromolecules - Link - PDF |
2013 |
SCI-E |
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Ngô Sơn Tùng và Mai Xuân Lý - Top-leads from natural products for treatment ofAlzheimer’s disease: Docking and molecular dynamics study - Molecular Simulation - Link - PDF |
2013 |
SCI-E |
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Phan Minh Truong, Man Hoang Viet, Phuong H. Nguyen, Chin-Kun Hu and Mai Suan Li - Effect of Taiwan Mutation (D7H) on Structures of Amyloid‑β Peptides: Replica Exchange Molecular Dynamics Study - The Journal of Physical Chemistry B - Link - PDF |
2014 |
SCI-E |
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Man Hoang Viet, Phuong H. Nguyen, Philippe Derreumaux and Mai Suan Li - Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of Aβ40 and Aβ42 - ACS Chemical Neuroscience - Link - PDF |
2014 |
SCI-E |
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Arthitaya Meeprasert, Thanyada Rungrotmongkol, Mai Suan Li and Supot Hannongbua - In Silico Screening for Potent Inhibitors against the NS3/4A Protease of Hepatitis C Virus - Current Pharmaceutical Design - Link - PDF |
2014 |
SCI-E |
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Hung Nguyen, Ly Le, and Tu Bao Ho - Computational study on ice growth inhibitor of Antarctic bacterium antifreeze protein using coarse grained simulation - The Journal of Chemical Physics - Link - PDF |
2014 |
SCI-E |
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Pham Dinh Quoc Huy and Mai Suan Li - Binding of fullerenes to amyloid beta fibrils: size matters - Physical Chemistry Chemical Physics - Link - PDF |
2014 |
SCI |
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Son Tung Ngo, Binh Khanh Mai, Dinh Minh Hiep and Mai Suan Li - Estimation of the Binding Free Energy of AC1NX476 to HIV-1 Protease Wild Type and Mutations Using Free Energy Perturbation Method - Chemical Biology & Drug Design - Link - PDF |
2015 |
SCI |
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Jessica Nasica-Labouze, Phuong H. Nguyen, Fabio Sterpone, Olivia Berthoumieu, Nicolae-Viorel Buchete, Sébastien Coté, Alfonso De Simone, Andrew J. Doig, Peter Faller, Angel Garcia, Alessandro Laio, Mai Suan Li, Simone Melchionna, Normand Mousseau,Yuguang Mu, Anant Paravastu, Samuela Pasquali, David J. Rosenman, Birgit Strodel,Bogdan Tarus, John H. Viles, Tong Zhang, Chunyu Wang, and Philippe Derreumaux - Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies - Chemical Reviews - Link - PDF |
2015 |
SCI |
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Maksim Kouza, Nguyen Truong Co, Phuong H. Nguyen, Andrzej Kolinski and Mai Suan Li - Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models - The Journal of Chemical Physics - Link - PDF |
2015 |
SCI |
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Man Hoang Viet, Katarina Siposova, Zuzana Bednarikova, Andrea Antosova, Truc Trang Nguyen, Zuzana Gazova, and Mai Suan Li - In Silico and in Vitro Study of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer’s Disease - The Journal of Physical Chemistry B - Link - PDF |
2015 |
SCI-E |
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Minh D. Pham, Ya-Ping Lin, Quan Van Vuong, Penumaka Nagababu, Brian T.-A. Chang, Kok Yaoh Ng, Chein-Hung Chen, Chau-Chung Han, Chung-Hsuan Chen, Mai Suan Li, g, Steve S.-F. Yu - Inactivation of the particulate methane monooxygenase (pMMO) in Methylococcus capsulatus (Bath) by acetylene - Biochimica et Biophysica Acta (BBA) - Proteins and Proteomic - Link - PDF |
2015 |
SCI-E |
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Man Hoang Viet, Phan Minh Truong, Philippe Derreumaux, Mai Suan Li, Christopher Roland, Celeste Sagui and Phuong H. Nguyen - Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study - Physical Chemistry Chemical Physics - Link - PDF |
2015 |
SCI-E |
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Man Hoang Viet, Philippe Derreumaux, Mai Suan Li, Christopher Roland, Celeste Sagui, and Phuong H. Nguyen - Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study - The Journal of Chemical Physics - Link - PDF |
2015 |
SCI-E |
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