Cargando…

AQDnet: Deep Neural Network for Protein–Ligand Docking Simulation

[Image: see text] We have developed an innovative system, AI QM Docking Net (AQDnet), which utilizes the three-dimensional structure of protein–ligand complexes to predict binding affinity. This system is novel in two respects: first, it significantly expands the training dataset by generating thous...

Descripción completa

Detalles Bibliográficos
Autores principales:	Shiota, Koji, Suma, Akira, Ogawa, Hiroyuki, Yamaguchi, Takuya, Iida, Akio, Hata, Takahiro, Matsushita, Mutsuyoshi, Akutsu, Tatsuya, Tateno, Masaru
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	American Chemical Society 2023
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10324054/ https://www.ncbi.nlm.nih.gov/pubmed/37426216 http://dx.doi.org/10.1021/acsomega.3c02411

Ejemplares similares

Conventional and novel impacts of ferric citrate on iron deficiency anemia and phosphorus metabolism in rats
por: IIDA, Akio, et al.
Publicado: (2020)

Multi-shelled ECIF: improved extended connectivity interaction features for accurate binding affinity prediction
por: Shiota, Koji, et al.
Publicado: (2023)

JTE-852, a novel spleen tyrosine kinase inhibitor, blocks antigen-induced allergic reactions in rats
por: KATO, Toshinobu, et al.
Publicado: (2018)

Improvement of spontaneous locomotor activity with JAK inhibition by JTE-052 in rat adjuvant-induced arthritis
por: Tanimoto, Atsuo, et al.
Publicado: (2015)

Quantum.Ligand.Dock: protein–ligand docking with quantum entanglement refinement on a GPU system
por: Kantardjiev, Alexander A.
Publicado: (2012)

CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein–ligand docking
por: Kwon, Sohee, et al.
Publicado: (2022)

CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction
por: Pang, Mingwei, et al.
Publicado: (2023)

Dockomatic - automated ligand creation and docking
por: Bullock, Casey W, et al.
Publicado: (2010)

Advances and Challenges in Protein-Ligand Docking
por: Huang, Sheng-You, et al.
Publicado: (2010)

The influence of protonation in protein-ligand docking
por: Brink, ten T, et al.
Publicado: (2008)

kinDOCK: a tool for comparative docking of protein kinase ligands
por: Martin, Laetitia, et al.
Publicado: (2006)

Pharmacological properties of JTE-052: a novel potent JAK inhibitor that suppresses various inflammatory responses in vitro and in vivo
por: Tanimoto, Atsuo, et al.
Publicado: (2014)

DINC: A new AutoDock-based protocol for docking large ligands
por: Dhanik, Ankur, et al.
Publicado: (2013)

Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking
por: Daldrop, Peter, et al.
Publicado: (2011)

Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand
por: DeLuca, Samuel, et al.
Publicado: (2015)

Internet Addiction and Attention-Deficit/Hyperactivity Disorder Traits among Female College Students in Japan
por: Tateno, Masaru, et al.
Publicado: (2018)

The protein flexibility in receptor-ligand docking simulations
por: Tristram, Frank
Publicado: (2010)

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

Comparative Analysis of Electrostatic Models for Ligand Docking
por: Sartori, Geraldo Rodrigues, et al.
Publicado: (2019)

Protein–Ligand Docking in the Machine-Learning Era
por: Yang, Chao, et al.
Publicado: (2022)

Combining fragment docking with graph theory to improve ligand docking for homology model structures
por: Sarfaraz, Sara, et al.
Publicado: (2020)

CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting
por: Liu, Yang, et al.
Publicado: (2022)

Evaluation of the Interaction between Long Telomeric DNA and Macrocyclic Hexaoxazole (6OTD) Dimer of a G-quadruplex Ligand
por: Iida, Keisuke, et al.
Publicado: (2013)

AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
por: Ravindranath, Pradeep Anand, et al.
Publicado: (2015)

CB-Dock: a web server for cavity detection-guided protein–ligand blind docking
por: Liu, Yang, et al.
Publicado: (2019)

In Silico Docking of HNF-1a Receptor Ligands
por: Sridhar, Gumpeny Ramachandra, et al.
Publicado: (2012)

Ligand-Enhanced Negative Images Optimized for Docking Rescoring
por: Kurkinen, Sami T., et al.
Publicado: (2022)

A molecular evolution algorithm for ligand design in DOCK
por: Prentis, Lauren E., et al.
Publicado: (2022)

Interaction of repaglinide with bovine serum albumin: Spectroscopic and molecular docking approaches
por: Pawar, Suma K., et al.
Publicado: (2019)

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina
por: Krause, Fabian, et al.
Publicado: (2023)

pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes
por: Khan, Javed Mohammed, et al.
Publicado: (2010)

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
por: Ruiz-Carmona, Sergio, et al.
Publicado: (2014)

Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
por: Cleves, Ann E., et al.
Publicado: (2015)

Predictive factors for dental inflammation with exacerbation during cancer therapy with FDG-PET/CT imaging
por: Kim, Mai, et al.
Publicado: (2021)

Pre-docking filter for protein and ligand 3D structures
por: Wilantho, Alisa, et al.
Publicado: (2008)

Guiding protein-ligand docking with different experimental NMR-data
por: ten Brink, Tim, et al.
Publicado: (2012)

A flexible-hydrogen interaction model for protein-ligand docking
por: Henzler, Angela M, et al.
Publicado: (2012)

The assessment of computationally derived protein ensembles in protein-ligand docking
por: Sander, Barbara, et al.
Publicado: (2012)

Development of target-biased scoring functions for protein-ligand docking
por: Scharfe, Michael, et al.
Publicado: (2012)

An interaction-motif-based scoring function for protein-ligand docking
por: Xie, Zhong-Ru, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_asg59muvrpig4fu6552cqfiiqa