Cargando…

Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M(pro) by Using Supervised Molecular Dynamics (SuMD) Simulations

Computational approaches supporting the early characterization of fragment molecular recognition mechanism represent a valuable complement to more expansive and low‐throughput experimental techniques. In this retrospective study, we have investigated the geometric accuracy with which high‐throughput...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bissaro, Maicol, Bolcato, Giovanni, Pavan, Matteo, Bassani, Davide, Sturlese, Mattia, Moro, Stefano
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley and Sons Inc. 2021
Materias:	Communications
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8250706/ https://www.ncbi.nlm.nih.gov/pubmed/33797868 http://dx.doi.org/10.1002/cmdc.202100156

Ejemplares similares

Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A(2A) Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations
por: Bissaro, Maicol, et al.
Publicado: (2019)

Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
por: Bissaro, Maicol, et al.
Publicado: (2020)

Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332
por: Pavan, Matteo, et al.
Publicado: (2021)

Investigating RNA–protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations
por: Pavan, Matteo, et al.
Publicado: (2022)

HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR
por: Ferrari, Francesca, et al.
Publicado: (2020)

A Computational Workflow for the Identification of Novel Fragments Acting as Inhibitors of the Activity of Protein Kinase CK1δ
por: Bolcato, Giovanni, et al.
Publicado: (2021)

Comparing Fragment Binding PosesPrediction Using HSP90 as a Key Study: When Bound Water Makes the Difference
por: Bolcato, Giovanni, et al.
Publicado: (2020)

Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics
por: Hassankalhori, Mahdi, et al.
Publicado: (2021)

New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations
por: Bolcato, Giovanni, et al.
Publicado: (2020)

Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir
por: Bolcato, Giovanni, et al.
Publicado: (2020)

The rise of molecular simulations in fragment-based drug design (FBDD): an overview
por: Bissaro, Maicol, et al.
Publicado: (2020)

Fighting Antimicrobial Resistance: Insights on How the Staphylococcus aureus NorA Efflux Pump Recognizes 2-Phenylquinoline Inhibitors by Supervised Molecular Dynamics (SuMD) and Molecular Docking Simulations
por: Palazzotti, Deborah, et al.
Publicado: (2023)

Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database
por: Bolcato, Giovanni, et al.
Publicado: (2019)

Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease M(pro)
por: Bassani, Davide, et al.
Publicado: (2022)

Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
por: Palazzotti, Deborah, et al.
Publicado: (2019)

Ribose and Non-Ribose A2A Adenosine Receptor Agonists: Do They Share the Same Receptor Recognition Mechanism?
por: Bolcato, Giovanni, et al.
Publicado: (2022)

The Hydrophobic Ligands Entry and Exit from the GPCR Binding Site-SMD and SuMD Simulations
por: Jakowiecki, Jakub, et al.
Publicado: (2020)

Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?
por: Pavan, Matteo, et al.
Publicado: (2022)

Sodium or Not Sodium: Should Its Presence Affect the Accuracy of Pose Prediction in Docking GPCR Antagonists?
por: Bassani, Davide, et al.
Publicado: (2022)

From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19?
por: Pavan, Matteo, et al.
Publicado: (2022)

Implementing a Scoring Function Based on Interaction Fingerprint for Autogrow4: Protein Kinase CK1δ as a Case Study
por: Pavan, Matteo, et al.
Publicado: (2022)

Qualitative Estimation of Protein–Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations
por: Pavan, Matteo, et al.
Publicado: (2022)

The Multifaceted Role of GPCRs in Amyotrophic Lateral Sclerosis: A New Therapeutic Perspective?
por: Bassani, Davide, et al.
Publicado: (2022)

Rethinking to riluzole mechanism of action: the molecular link among protein kinase CK1δ activity, TDP-43 phosphorylation, and amyotrophic lateral sclerosis pharmacological treatment
por: Bissaro, Maicol, et al.
Publicado: (2019)

A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection
por: Jiménez-Luna, José, et al.
Publicado: (2020)

Drugging the Undruggable Trypanosoma brucei Monothiol Glutaredoxin 1
por: Favaro, Annagiulia, et al.
Publicado: (2023)

Health Supervision and Medical Inspection of Schools
Publicado: (1928)

Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement
por: Menin, Silvia, et al.
Publicado: (2023)

Medical Inspection and Supervision of School Children in Edinburgh
por: Meikle, J. Hally
Publicado: (1917)

Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes
por: Dodaro, Andrea, et al.
Publicado: (2023)

SICT: automated detection and supervised inspection of fast Ca(2+) transients
por: Mancini, Roberta, et al.
Publicado: (2018)

Acoustic Inspection of Concrete Structures Using Active Weak Supervision and Visual Information
por: Louhi Kasahara, Jun Younes, et al.
Publicado: (2020)

Structural Analysis and Development of Notum Fragment Screening Hits
por: Zhao, Yuguang, et al.
Publicado: (2022)

PAC-FragmentDEL – photoactivated covalent capture of DNA-encoded fragments for hit discovery
por: Ma, Huiyong, et al.
Publicado: (2022)

Semi-Supervised Defect Detection Method with Data-Expanding Strategy for PCB Quality Inspection
por: Wan, Yusen, et al.
Publicado: (2022)

Solvents to Fragments to Drugs: MD Applications in Drug Design
por: Defelipe, Lucas A., et al.
Publicado: (2018)

On the mechanism of tumor cell entry of aloe‐emodin, a natural compound endowed with anticancer activity
por: Pecere, Teresa, et al.
Publicado: (2021)

Low energy transversal - PS suffexion acier SU/MD
por: Potier, JP
Publicado: (1979)

La Auditoría en su fase de supervisión
por: Cano Ruíz, Dulce María
Publicado: (1988)

Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking
por: Metz, Alexander, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_9msrc9hub9goaf8c5esiu4bv41