4.7 Article

Can de-phosphorylation of serine-5 in the C-terminal domain of human polymerase II affect its interaction with the PA C-terminal domain of bat Flu A polymerase?

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2

Gideon A. Gyebi et al.

Summary: In silico studies were conducted to evaluate 97 alkaloids from African medicinal plants for their interactions with SARS-CoV-2 related proteins. Results showed that more than 15 alkaloids exhibited strong interactions with these proteins, suggesting their potential in altering the virus's ability to enter host cells. Further experimental evaluations are proposed.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

Article Biochemistry & Molecular Biology

Structure-based identification of potential SARS-CoV-2 main protease inhibitors

Shama Khan et al.

Summary: To address the lack of effective drugs or vaccines for COVID-19, researchers used molecular modeling methods to discover potential inhibitors of the SARS-CoV-2 M-pro enzyme. Through simulation studies, they identified five potential inhibitors, one of which showed high affinity and stability in binding to the M-pro. These compounds could be promising candidates for COVID-19 therapy, but further experimental and clinical validation is needed.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2022)

Article Biochemistry & Molecular Biology

The anti-HCV, Sofosbuvir, versus the anti-EBOV Remdesivir against SARS-CoV-2 RNA dependent RNA polymerase in silico

Abdo A. Elfiky et al.

Summary: This study evaluates the binding affinity of the clinically approved drug sofosbuvir with the viral protein RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 using molecular docking and dynamics simulations. Sofosbuvir demonstrates effective binding with the RdRp target, making it a potential therapeutic option against COVID-19, comparable to the FDA-approved drug Remdesivir.

MOLECULAR DIVERSITY (2022)

Article Chemistry, Multidisciplinary

Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase

Abdo A. Elfiky et al.

Summary: This study utilizes molecular dynamics simulation and molecular docking to test novel guanosine derivatives against SARS-CoV-2 RdRp. Results show that these derivatives have strong binding affinity to the viral structures, suggesting their potential as new blockers of SARS-CoV-2.

RSC ADVANCES (2022)

Article Biochemistry & Molecular Biology

PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA

Melissa F. Adasme et al.

Summary: With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules becomes increasingly important. PLIP, a tool for protein-ligand interaction profiling, has been successful in detecting and visualizing these interactions, with applications ranging from characterizing docking experiments to evaluating novel ligand-protein complexes. Additionally, PLIP has been extended to encompass interactions with DNA and RNA, demonstrating its utility in scenarios such as cancer drug targeting DNA and RNA-protein complexes associated with neurological diseases.

NUCLEIC ACIDS RESEARCH (2021)

Article Medicine, Research & Experimental

Structure and Function of the Influenza Virus Transcription and Replication Machinery

Ervin Fodor et al.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2020)

Review Biochemistry & Molecular Biology

Interplay between Influenza Virus and the Host RNA Polymerase II Transcriptional Machinery

Alexander P. Walker et al.

TRENDS IN MICROBIOLOGY (2019)

Article Virology

Initiation, Elongation, and Realignment during Influenza Virus mRNA Synthesis

Aartjan J. W. te Velthuis et al.

JOURNAL OF VIROLOGY (2018)

Review Pharmacology & Pharmacy

Influenza A virus polymerase: an attractive target for next-generation anti-influenza therapeutics

Zhongxia Zhou et al.

DRUG DISCOVERY TODAY (2018)

Article Medicine, General & Internal

Influenza

Florian Krammer et al.

NATURE REVIEWS DISEASE PRIMERS (2018)

Article Chemistry, Medicinal

TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries

Thibault Tubiana et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2018)

Article Multidisciplinary Sciences

Structural basis of an essential interaction between influenza polymerase and Pol II CTD

Maria Lukarska et al.

NATURE (2017)

Article Biochemical Research Methods

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

Li C. Xue et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

G. C. P. van Zundert et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Article Chemistry, Medicinal

IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study

Abdo A. Elfiky et al.

MEDICINAL CHEMISTRY RESEARCH (2016)

Review Microbiology

Influenza virus RNA polymerase: insights into the mechanisms of viral RNA synthesis

Aartjan J. W. te Velthuis et al.

NATURE REVIEWS MICROBIOLOGY (2016)

Review Microbiology

Influenza B viruses: not to be discounted

Carolien E. van de Sandt et al.

FUTURE MICROBIOLOGY (2015)

Review Biochemistry & Molecular Biology

Bat-derived influenza-like viruses H17N10 and H18N11

Ying Wu et al.

TRENDS IN MICROBIOLOGY (2014)

Article Multidisciplinary Sciences

Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1

Spencer O. Moen et al.

SCIENTIFIC REPORTS (2014)

Article Chemistry, Multidisciplinary

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Marcus D. Hanwell et al.

JOURNAL OF CHEMINFORMATICS (2012)

Article Biochemical Research Methods

MolProbity: all-atom structure validation for macromolecular crystallography

Vincent B. Chen et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Ligand docking and binding site analysis with PyMOL and Autodock/Vina

Daniel Seeliger et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2010)

Article Chemistry, Physical

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

M. J. Harvey et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Review Chemistry, Multidisciplinary

Scalable molecular dynamics with NAMD

JC Phillips et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)