Cargando…

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtain...

Descripción completa

Detalles Bibliográficos
Autores principales:	Okimoto, Noriaki, Futatsugi, Noriyuki, Fuji, Hideyoshi, Suenaga, Atsushi, Morimoto, Gentaro, Yanai, Ryoko, Ohno, Yousuke, Narumi, Tetsu, Taiji, Makoto
Formato:	Texto
Lenguaje:	English
Publicado:	Public Library of Science 2009
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746282/ https://www.ncbi.nlm.nih.gov/pubmed/19816553 http://dx.doi.org/10.1371/journal.pcbi.1000528

Ejemplares similares

Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation
por: Komatsu, Teruhisa S., et al.
Publicado: (2020)

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model
por: Yamagishi, Junya, et al.
Publicado: (2014)

MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations
por: Ohmura, Itta, et al.
Publicado: (2014)

An Efficient Computational Method for Calculating Ligand Binding Affinities
por: Suenaga, Atsushi, et al.
Publicado: (2012)

Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein–Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors
por: Okimoto, Noriaki, et al.
Publicado: (2018)

Molecular Dynamics Study of Conformational Changes of Tankyrase 2 Binding Subsites upon Ligand Binding
por: Hirano, Yoshinori, et al.
Publicado: (2021)

Large-scale all-atom molecular dynamics alanine-scanning of IAPP octapeptides provides insights into the molecular determinants of amyloidogenicity
por: Tambi, Richa, et al.
Publicado: (2019)

FGF9 monomer/dimer equilibrium regulates extracellular matrix affinity and tissue diffusion
por: Harada, Masayo, et al.
Publicado: (2009)

Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH
por: Sato, Ryuma, et al.
Publicado: (2020)

All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations
por: Kuroda, Yutaka, et al.
Publicado: (2016)

Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies
por: Berishvili, Vladimir P., et al.
Publicado: (2020)

Based on the Virtual Screening of Multiple Pharmacophores, Docking and Molecular Dynamics Simulation Approaches toward the Discovery of Novel HPPD Inhibitors
por: Fu, Ying, et al.
Publicado: (2020)

mPGES-1 Inhibitor Discovery Based on Computer-Aided Screening: Pharmacophore Models, Molecular Docking, ADMET, and MD Simulations
por: Huang, Qiqi, et al.
Publicado: (2023)

Discovery of novel RARα agonists using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulation studies
por: Ghorayshian, Atefeh, et al.
Publicado: (2023)

Discovery of YopE Inhibitors by Pharmacophore-Based Virtual Screening and Docking
por: Ozbuyukkaya, Gizem, et al.
Publicado: (2013)

The Discovery of Aurora Kinase Inhibitor by Multi-Docking-Based Virtual Screening
por: Kim, Jun-Tae, et al.
Publicado: (2014)

Molecular Docking: Shifting Paradigms in Drug Discovery
por: Pinzi, Luca, et al.
Publicado: (2019)

Discovery of New VEGFR-2 Inhibitors: Design, Synthesis, Anti-Proliferative Evaluation, Docking, and MD Simulation Studies
por: Elkaeed, Eslam B., et al.
Publicado: (2022)

Survey of public domain software for docking simulations and virtual screening
por: Biesiada, Jacek, et al.
Publicado: (2011)

Transcriptome profiles of rice roots under simulated microgravity conditions and following gravistimulation
por: Kuya, Noriyuki, et al.
Publicado: (2023)

Covalent Docking of Large Libraries for the Discovery of Chemical Probes
por: London, Nir, et al.
Publicado: (2014)

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

Discovery of novel phthalimide analogs: Synthesis, antimicrobial and antitubercular screening with molecular docking studies
por: Rateb, Heba S., et al.
Publicado: (2016)

Distinction between Chronic Enteropathy Associated with the SLCO2A1 Gene and Crohn’s Disease
por: Yanai, Shunichi, et al.
Publicado: (2019)

Design of a New α-1-C-Alkyl-DAB Derivative Acting as a Pharmacological Chaperone for β-Glucocerebrosidase Using Ligand Docking and Molecular Dynamics Simulation
por: Nakagome, Izumi, et al.
Publicado: (2018)

DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations
por: Cuzzolin, Alberto, et al.
Publicado: (2015)

O-Glycan-Dependent Interaction between MUC1 Glycopeptide and MY.1E12 Antibody by NMR, Molecular Dynamics and Docking Simulations
por: Kokubu, Ryoka, et al.
Publicado: (2022)

Discovery of Some Heterocyclic Molecules as Bone Morphogenetic Protein 2 (BMP-2)-Inducible Kinase Inhibitors: Virtual Screening, ADME Properties, and Molecular Docking Simulations
por: Belal, Amany, et al.
Publicado: (2022)

From Myricetin to the Discovery of Novel Natural Human ENPP1 Inhibitors: A Virtual Screening, Molecular Docking, Molecular Dynamics Simulation, and MM/GBSA Study
por: Song, Shaohan, et al.
Publicado: (2022)

Discovery of anti-MERS-CoV small covalent inhibitors through pharmacophore modeling, covalent docking and molecular dynamics simulation
por: Alamri, Mubarak A., et al.
Publicado: (2021)

Discovery of potential natural dihydroorotate dehydrogenase inhibitors and their synergism with brequinar via integrated molecular docking, dynamic simulations and in vitro approach
por: Khairy, Asmaa, et al.
Publicado: (2022)

Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Discovery of Novel Akt2 Inhibitors
por: Fei, Jia, et al.
Publicado: (2013)

Discovery of Oxime Ethers as Hepatitis B Virus (HBV) Inhibitors by Docking, Screening and In Vitro Investigation
por: Tan, Jie, et al.
Publicado: (2018)

Discovery of High Affinity Receptors for Dityrosine through Inverse Virtual Screening and Docking and Molecular Dynamics
por: Wang, Fangfang, et al.
Publicado: (2018)

Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
por: Gioia, Dario, et al.
Publicado: (2017)

Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls
por: Kumalo, Hezekiel Mathambo, et al.
Publicado: (2015)

Coronavirus disease 2019 drug discovery through molecular docking
por: Singh, Sweta, et al.
Publicado: (2020)

A pre-metazoan origin of the CRK gene family and co-opted signaling network
por: Shigeno-Nakazawa, Yoko, et al.
Publicado: (2016)

Identification of novel PTPRQ phosphatase inhibitors based on the virtual screening with docking simulations
por: Park, Hwangseo, et al.
Publicado: (2013)

Discovery of Klotho peptide antagonists against Wnt3 and Wnt3a target proteins using combination of protein engineering, protein–protein docking, peptide docking and molecular dynamics simulations
por: Mirza, Shaher Bano, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_jajn6kehjrnjufa9oui41iiqs8