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64 Results       Page 1

 [1] 
American Chemical Society: The Journal of Physical Chemistry B
  original article Date Title Authors   All Authors
1 [GO] 2025―Jan―31 In Silico Discovery of SARS-CoV-2 Main Protease Inhibitors Using Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations Takeshi Ishikawa, Kenji Matsumoto, Toshiyuki Hamada, Hinako Koze, Masanori Baba, Mika Okamoto, Masayuki Sudoh
2 [GO] 2024―Dec―18 Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics Sahil Lall, Padmanabhan Balaram, M. K. Mathew, Shachi Gosavi
3 [GO] 2024―Dec―03 Identification of RdRp-NiRAN/JAK1 Dual-Target Drugs for COVID-19 Treatment Huixuan Zhao, Xiaoyu Chang, Lei Sun, Ertong Li, Depeng Zhang, Wentao Qi, et al. (+3)
4 [GO] 2024―Jul―16 Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations Hoang Linh Nguyen, Ho Khac Hieu, Thai Quoc Nguyen, Nguyen Thi Ai Nhung, Mai Suan Li
5 [GO] 2024―Jul―15 Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation Hung Nguyen, Hoang Linh Nguyen, Mai Suan Li
6 [GO] 2024―May―02 AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker
7 [GO] 2024―Apr―24 A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2 Lalita Mohan Behera, Pulkit Kr. Gupta, Manaswini Ghosh, Sucharita Shadangi, Soumendra Rana
8 [GO] 2024―Apr―02 SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study Hoang Linh Nguyen, Thai Quoc Nguyen, Mai Suan Li
9 [GO] 2024―Mar―11 Bis(Monoacylglycero)Phosphate Promotes Membrane Fusion Facilitated by the SARS-CoV-2 Fusion Domain Daniel Birtles, Wafa Abbas, Jinwoo Lee
10 [GO] 2024―Mar―04 Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, et al. (+5)
11 [GO] 2024―Jan―08 Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain Michele Monti, Edoardo Milanetti, Myrthe T. Frans, Mattia Miotto, Lorenzo Di Rienzo, Maksim V. Baranov, et al. (+13)
12 [GO] 2024―Jan―04 Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13 Monsurat M. Lawal, Priti Roy, Martin McCullagh
13 [GO] 2023―Dec―26 Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2 Min-Kang Hsieh, Jeffery B. Klauda
14 [GO] 2023―Oct―10 From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics Aditya K. Padhi, Parismita Kalita, Shweata Maurya, Krishna Mohan Poluri, Timir Tripathi
15 [GO] 2023―Sep―29 Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein Mariem Ghoula, Audrey Deyawe Kongmeneck, Rita Eid, Anne-Claude Camproux, Gautier Moroy
16 [GO] 2023―Sep―28 Riding the Wave: Unveiling the Conformational Waves from RBD of SARS-CoV-2 Spike Protein to ACE2 Nikhil Maroli
17 [GO] 2023―Sep―27 Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV-2 Spike Indicate a Barrierless Transition with Slow Conformational Motions Victor Ovchinnikov, Martin Karplus
18 [GO] 2023―Sep―22 Intrinsically Disordered Regions Function as a Cervical Collar to Remotely Regulate the Nodding Dynamics of SARS-CoV-2 Prefusion Spike Heads Anushree Sinha, Susmita Roy
19 [GO] 2023―Jul―31 Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1 Tanushree Das, Chaitali Mukhopadhyay
20 [GO] 2023―May―17 Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein Peng Liu, Yao Li, Yawei Liu, Ju Liu, Kun Dong, Qingzhu Jia
21 [GO] 2023―May―12 Adsorption of SARS-CoV-2 Spike (N501Y) RBD to Human Angiotensin-Converting Enzyme 2 at a Lipid/Water Interface Harison Rozak, Satoshi Nihonyanagi, Anton Myalitsin, Subhadip Roy, Mohammed Ahmed, Tahei Tahara, Izabela I. Rzeznicka
22 [GO] 2023―Mar―13 Biophysical Interpretation of Evolutionary Consequences on the SARS-CoV2 Main Protease through Molecular Dynamics Simulations and Network Topology Analysis Nuttawat Sawang, Saree Phongphanphanee, Jirasak Wong-ekkabut, Thana Sutthibutpong
23 [GO] 2023―Feb―24 Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization Matthew C. Chan, Kui. K. Chan, Erik Procko, Diwakar Shukla
24 [GO] 2023―Feb―15 Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2 Kawkab Kanjo, Gopinath Chattopadhyay, Sameer Kumar Malladi, Randhir Singh, Sowrabha Jayatheertha, Raghavan Varadarajan
25 [GO] 2023―Jan―23 Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease Arkadeep Banerjee, Shachi Gosavi
26 [GO] 2022―Oct―11 Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors Sudeep Sarma, Stephanie M. Herrera, Xingqing Xiao, Gregory A. Hudalla, Carol K. Hall
27 [GO] 2022―Sep―30 Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method Satyam Sangeet, Raju Sarkar, Saswat K. Mohanty, Susmita Roy
28 [GO] 2022―Sep―06 Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule Fernando L. Barroso da Silva, Carolina Corrêa Giron, Aatto Laaksonen
29 [GO] 2022―Jul―14 All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes Saheb Dutta, Bhavana Panthi, Amalendu Chandra
30 [GO] 2022―Jul―12 Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning Alexander H. Williams, Chang-Guo Zhan
31 [GO] 2022―Jun―23 Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains Tong Li, Lan Yu, Jingfang Sun, Jinfeng Liu, Xiao He
32 [GO] 2022―Jun―20 SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation Hoang Linh Nguyen, Nguyen Quoc Thai, Phuong H. Nguyen, Mai Suan Li
33 [GO] 2022―Jun―06 Different Binding Modes of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides to Cell Membranes: The Influence of Peptide Helix Length Hujun Shen, Zhenhua Wu, Ling Chen
34 [GO] 2022―May―17 Effect of an Amyloidogenic SARS-COV-2 Protein Fragment on α-Synuclein Monomers and Fibrils Asis K. Jana, Chance W. Lander, Andrew D. Chesney, Ulrich H. E. Hansmann
35 [GO] 2022―Apr―11 Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Mai Suan Li
36 [GO] 2022―Mar―22 Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II Alexander H. Williams, Chang-Guo Zhan
37 [GO] 2022―Mar―10 Combined Computational NMR and Molecular Docking Scrutiny of Potential Natural SARS-CoV-2 Mpro Inhibitors Valentin A. Semenov, Leonid B. Krivdin
38 [GO] 2022―Jan―04 Detection of Covid-19 through a Heptanal Biomarker Using Transition Metal Doped Graphene Anthony Zhu, Xuan Luo
39 [GO] 2021―Dec―14 In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease Kamonpan Sanachai, Panupong Mahalapbutr, Vannajan Sanghiran Lee, Thanyada Rungrotmongkol, Supot Hannongbua
40 [GO] 2021―Sep―27 Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations Solène Lecot, Yann Chevolot, Magali Phaner-Goutorbe, Christelle Yeromonahos
41 [GO] 2021―Sep―21 Bioactive Ag3PO4/Polypropylene Composites for Inactivation of SARS-CoV-2 and Other Important Public Health Pathogens Lara K. Ribeiro, Marcelo Assis, Lais R. Lima, Dyovani Coelho, Mariana O. Gonçalves, Robert S. Paiva, et al. (+11)
42 [GO] 2021―Aug―09 Presence of a SARS-CoV-2 Protein Enhances Amyloid Formation of Serum Amyloid A Asis K. Jana, Augustus B. Greenwood, Ulrich H. E. Hansmann
43 [GO] 2021―Jul―30 Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase Ryan Weber, Martin McCullagh
44 [GO] 2021―Jul―28 Accelerating COVID-19 Research Using Molecular Dynamics Simulation Aditya K. Padhi, Soumya Lipsa Rath, Timir Tripathi
45 [GO] 2021―Jul―23 Structural Decoding of a Small Molecular Inhibitor on the Binding of SARS-CoV-2 to the ACE 2 Receptor Pushpendra Mani Mishra, Chayan Kanti Nandi
46 [GO] 2021―Jul―13 Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane Stefan L. Schaefer, Hendrik Jung, Gerhard Hummer
47 [GO] 2021―Jul―06 Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Mai Suan Li
48 [GO] 2021―Jun―11 Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study Luana Janaína de Campos, Nicholas Y. Palermo, Martin Conda-Sheridan
49 [GO] 2021―Jun―10 Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351 Nisha Bhattarai, Prabin Baral, Bernard S. Gerstman, Prem P. Chapagain
50 [GO] 2021―May―12 Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor Elhan Taka, Sema Z. Yilmaz, Mert Golcuk, Ceren Kilinc, Umut Aktas, Ahmet Yildiz, Mert Gur
51 [GO] 2021―Apr―30 Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies Gennady M. Verkhivker, Luisa Di Paola
52 [GO] 2021―Apr―23 Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates Alexander H. Williams, Chang-Guo Zhan
53 [GO] 2021―Mar―03 An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2 Billy J. Williams-Noonan, Nevena Todorova, Ketav Kulkarni, Marie-Isabel Aguilar, Irene Yarovsky
54 [GO] 2021―Jan―15 Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches Gennady M. Verkhivker, Luisa Di Paola
55 [GO] 2020―Dec―02 Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations Hoang Linh Nguyen, Nguyen Quoc Thai, Duc Toan Truong, Mai Suan Li
56 [GO] 2020―Nov―17 Computational Design of 25-mer Peptide Binders of SARS-CoV-2 Thassanai Sitthiyotha, Surasak Chunsrivirot
57 [GO] 2020―Nov―15 Revealing the Inhibition Mechanism of RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2 by Remdesivir and Nucleotide Analogues: A Molecular Dynamics Simulation Study Padmaja D. Wakchaure, Shibaji Ghosh, Bishwajit Ganguly
58 [GO] 2020―Nov―11 How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration Hossein Eslami, Shubhadip Das, Tianhang Zhou, Florian Müller-Plathe
59 [GO] 2020―Oct―28 Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations Mahdi Ghorbani, Bernard R. Brooks, Jeffery B. Klauda
60 [GO] 2020―Oct―23 Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 Surid Mohammad Chowdhury, Shafi Ahmad Talukder, Akib Mahmud Khan, Nadia Afrin, Md Ackas Ali, Rajib Islam, et al. (+6)
61 [GO] 2020―Jul―29 Does SARS-CoV-2 Bind to Human ACE2 Stronger Than SARS-CoV? Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Daniel A. Nissley, Edward P. O'Brien, Mai Suan Li
62 [GO] 2020―Jun―19 Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, et al. (+6)
63 [GO] 2020―Jun―17 Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV Chen Bai, Arieh Warshel
64 [GO] 2020―Jun―10 Structural basis of potential binding mechanism of remdesivir to SARS-CoV-2 RNA dependent RNA polymerase Leili Zhang, Ruhong Zhou
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64 Results       Page 1


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