Cargando…

Identifying and sampling conformational states of SARS-CoV-2 m(pro) for flexible receptor docking

Detalles Bibliográficos
Autores principales:	Smith, Matthew S., Grabe, Michael, Shoichet, Brian
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Biophysical Society. Published by Elsevier Inc. 2023
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912779/ http://dx.doi.org/10.1016/j.bpj.2022.11.893

Ejemplares similares

The incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery
por: Fischer, Marcus, et al.
Publicado: (2014)

Sampling the conformation of protein surface residues for flexible protein docking
por: Francis-Lyon, Patricia, et al.
Publicado: (2010)

Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV M(pro)
por: Niu, Chunying, et al.
Publicado: (2008)

Ligand Pose and Orientational Sampling in Molecular Docking
por: Coleman, Ryan G., et al.
Publicado: (2013)

Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock
por: Torchala, Mieczyslaw, et al.
Publicado: (2019)

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M(pro))
por: Ebrahim, Ali, et al.
Publicado: (2021)

Molecular docking analysis of selected phytochemicals against SARS-CoV-2 M(pro) receptor
por: Garg, Saksham, et al.
Publicado: (2020)

The Impact of Introducing a Histidine into an Apolar Cavity Site on Docking and Ligand Recognition
por: Merski, Matthew, et al.
Publicado: (2013)

pH-dependent Conformational Flexibility of the SARS-CoV Main Proteinase (M(pro)) Dimer: Molecular Dynamics Simulations and Multiple X-ray Structure Analyses
por: Tan, Jinzhi, et al.
Publicado: (2005)

Conformational flexibility and structural variability of SARS-CoV2 S protein
por: Pramanick, Ishika, et al.
Publicado: (2021)

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M(pro))
por: Ebrahim, Ali, et al.
Publicado: (2022)

Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 M(pro), using molecular docking and dynamics simulation studies
por: Ahamad, Shahzaib, et al.
Publicado: (2021)

Potential Inhibitors of SARS-CoV-2 Main Protease (M(pro)) Identified from the Library of FDA-Approved Drugs Using Molecular Docking Studies
por: Verma, Dipesh Kumar, et al.
Publicado: (2022)

Optimization Rules for SARS-CoV-2 M(pro) Antivirals: Ensemble Docking and Exploration of the Coronavirus Protease Active Site
por: Stoddard, Shana V., et al.
Publicado: (2020)

Azaphenantherene derivatives as inhibitor of SARS CoV-2 M(pro): Synthesis, physicochemical, quantum chemical and molecular docking analysis
por: Venkateshan, M., et al.
Publicado: (2020)

Prediction of Novel Inhibitors of the Main Protease (M-pro) of SARS-CoV-2 through Consensus Docking and Drug Reposition
por: Gimeno, Aleix, et al.
Publicado: (2020)

Drugs Repurposing Using QSAR, Docking and Molecular Dynamics for Possible Inhibitors of the SARS-CoV-2 M(pro) Protease
por: Tejera, Eduardo, et al.
Publicado: (2020)

Conformational flexibility in neutralization of SARS-CoV-2 by naturally elicited anti-SARS-CoV-2 antibodies
por: Li, Ruofan, et al.
Publicado: (2022)

Conformation Guides Molecular Efficacy in Docking Screens of Activated β-2 Adrenergic G Protein Coupled Receptor
por: Weiss, Dahlia R., et al.
Publicado: (2013)

IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States
por: Teixeira, João M. C., et al.
Publicado: (2022)

Modeling conformational flexibility of kinases in inactive states
por: Schwarz, Dominik, et al.
Publicado: (2019)

Docking for molecules that bind in a symmetric stack with SymDOCK
por: Smith, Matthew S., et al.
Publicado: (2023)

Performance evaluation of flexible macrocycle docking in AutoDock
por: Holcomb, Matthew, et al.
Publicado: (2022)

DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins
por: Hall-Swan, Sarah, et al.
Publicado: (2021)

Effect of conformation sampling strategies in genetic algorithm for multiple protein docking
por: Esquivel-Rodríguez, Juan, et al.
Publicado: (2012)

SARS-CoV2 billion-compound docking
por: Rogers, David M., et al.
Publicado: (2023)

Machine learning prediction of 3CL(pro) SARS-CoV-2 docking scores
por: Bucinsky, Lukas, et al.
Publicado: (2022)

Docking-based virtual screening studies aiming at the covalent inhibition of SARS-CoV-2 M(Pro) by targeting the cysteine 145
por: Soulère, Laurent, et al.
Publicado: (2021)

In-silico study: docking simulation and molecular dynamics of peptidomimetic fullerene-based derivatives against SARS-CoV-2 M(pro)
por: Saleh, Noha A.
Publicado: (2023)

Discovery of PL(pro) and M(pro) Inhibitors for SARS-CoV-2
por: Puhl, Ana C., et al.
Publicado: (2023)

Anticoagulants as Potential SARS-CoV-2 M(pro) Inhibitors for COVID-19 Patients: In Vitro, Molecular Docking, Molecular Dynamics, DFT, and SAR Studies
por: Abo Elmaaty, Ayman, et al.
Publicado: (2022)

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking
por: Schuller, Marion, et al.
Publicado: (2020)

Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds
por: Chaput, Ludovic, et al.
Publicado: (2017)

Molecular docking, molecular dynamics simulation, and ADMET analysis of levamisole derivatives against the SARS-CoV-2 main protease (M(Pro))
por: EL Khatabi, Khalil, et al.
Publicado: (2022)

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking
por: Schuller, Marion, et al.
Publicado: (2021)

Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL(pro) and M(pro)/ 3CL(pro): molecular docking and simulation studies of three pertinent medicinal plant natural components
por: Verma, Devvret, et al.
Publicado: (2021)

β-Lactoglobulin's Conformational Requirements for Ligand Binding at the Calyx and the Dimer Interphase: a Flexible Docking Study
por: Domínguez-Ramírez, Lenin, et al.
Publicado: (2013)

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins
por: Devaurs, Didier, et al.
Publicado: (2019)

Distinct conformational states of SARS-CoV-2 spike protein
por: Cai, Yongfei, et al.
Publicado: (2020)

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (M(pro)) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study
por: Tallei, Trina Ekawati, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_8651gke8sp51n64r8mjq6hnnj0