Cargando…

GalaxySite: ligand-binding-site prediction by using molecular docking

Knowledge of ligand-binding sites of proteins provides invaluable information for functional studies, drug design and protein design. Recent progress in ligand-binding-site prediction methods has demonstrated that using information from similar proteins of known structures can improve predictions. T...

Descripción completa

Detalles Bibliográficos
Autores principales:	Heo, Lim, Shin, Woong-Hee, Lee, Myeong Sup, Seok, Chaok
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2014
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086128/ https://www.ncbi.nlm.nih.gov/pubmed/24753427 http://dx.doi.org/10.1093/nar/gku321

Ejemplares similares

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
por: Lee, Hasup, et al.
Publicado: (2015)

Galaxy7TM: flexible GPCR–ligand docking by structure refinement
por: Lee, Gyu Rie, et al.
Publicado: (2016)

HProteome-BSite: predicted binding sites and ligands in human 3D proteome
por: Sim, Jiho, et al.
Publicado: (2022)

GalaxyWEB server for protein structure prediction and refinement
por: Ko, Junsu, et al.
Publicado: (2012)

GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
por: Park, Taeyong, et al.
Publicado: (2021)

GalaxyRefine: protein structure refinement driven by side-chain repacking
por: Heo, Lim, et al.
Publicado: (2013)

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking
por: Heo, Lim, et al.
Publicado: (2016)

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

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking
por: Wu, Qi, et al.
Publicado: (2018)

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure
por: Baek, Minkyung, et al.
Publicado: (2017)

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
por: Lee, Gyu Rie, et al.
Publicado: (2019)

Structural and Molecular Docking Analytical Studies of the Predicted Ligand Binding Sites of Cadherin-1 in Cancer Prognostics
por: Bakare, Olalekan Olanrewaju, et al.
Publicado: (2020)

Ligand docking and binding site analysis with PyMOL and Autodock/Vina
por: Seeliger, Daniel, et al.
Publicado: (2010)

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

Automatic docking of a small number of ligands into a large number of binding sites
por: Kos, Alexander
Publicado: (2013)

3DLigandSite: predicting ligand-binding sites using similar structures
por: Wass, Mark N., et al.
Publicado: (2010)

3DLigandSite: structure-based prediction of protein–ligand binding sites
por: McGreig, Jake E, et al.
Publicado: (2022)

Structural Studies of Predicted Ligand Binding Sites and Molecular Docking Analysis of Slc2a4 as a Therapeutic Target for the Treatment of Cancer
por: Aruleba, Raphael Taiwo, et al.
Publicado: (2018)

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
por: Ko, Junsu, et al.
Publicado: (2012)

Prediction of Protein Ion–Ligand Binding Sites with ELECTRA
por: Essien, Clement, et al.
Publicado: (2023)

LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites
por: Xie, Zhong-Ru, et al.
Publicado: (2013)

From complete cross-docking to partners identification and binding sites predictions
por: Dequeker, Chloé, et al.
Publicado: (2022)

Predicting target-ligand interactions using protein ligand-binding site and ligand substructures
por: Wang, Caihua, et al.
Publicado: (2015)

An alternate binding site for PPARγ ligands
por: Hughes, Travis S., et al.
Publicado: (2014)

Exploring the computational methods for protein-ligand binding site prediction
por: Zhao, Jingtian, et al.
Publicado: (2020)

Are nuclear hotspots in galaxies sites of sequential star formation?
por: Korchagin, Yu V, et al.
Publicado: (1994)

Docking Server for the Identification of Heparin Binding Sites on Proteins
por: Mottarella, Scott E., et al.
Publicado: (2014)

GraphSite: Ligand Binding Site Classification with Deep Graph Learning
por: Shi, Wentao, et al.
Publicado: (2022)

Characteristics of the Protoporphyrin IX Binding Sites on Human Serum Albumin Using Molecular Docking
por: Sułkowski, Leszek, et al.
Publicado: (2016)

In Silico Docking, Molecular Dynamics and Binding Energy Insights into the Bolinaquinone-Clathrin Terminal Domain Binding Site
por: Abdel-Hamid, Mohammed K., et al.
Publicado: (2014)

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

Predicting small ligand binding sites in proteins using backbone structure
por: Bordner, Andrew J.
Publicado: (2008)

Comparison of Different Ranking Methods in Protein-Ligand Binding Site Prediction
por: Gao, Jun, et al.
Publicado: (2012)

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
por: Komiyama, Yusuke, et al.
Publicado: (2016)

Sequence variation in ligand binding sites in proteins
por: Magliery, Thomas J, et al.
Publicado: (2005)

PSnpBind-ML: predicting the effect of binding site mutations on protein-ligand binding affinity
por: Ammar, Ammar, et al.
Publicado: (2023)

How to Use Not-Always-Reliable Binding Site Information in Protein-Protein Docking Prediction
por: Li, Lin, et al.
Publicado: (2013)

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites
por: Konc, Janez, et al.
Publicado: (2014)

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

Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation
por: Vidad, Ashley Ryan, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_1tqreph5mbfa6c11endi9h89sp