ArticleNucleic acids research2014
GalaxySite: ligand-binding-site prediction by using molecular docking.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Insights into Octopus maya cathepsins from metatranscriptome and genome: structure evolutionary relationships and functional role prediction in digestive processes.Biology open · 2025Article
- Improving Identification of Drug-Target Binding Sites Based on Structures of Targets Using Residual Graph Transformer Network.Biomolecules · 2025Article
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- An ancient bacterial zinc acquisition system identified from a cyanobacterial exoproteome.PLoS biology · 2024Article
- Cobdock: an accurate and practical machine learning-based consensus blind docking method.Journal of cheminformatics · 2024Article
- HProteome-BSite: predicted binding sites and ligands in human 3D proteome.Nucleic acids research · 2023Article
- Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.Computational and structural biotechnology journal · 2023Article
- In silico analysis of a Skp1 protein homolog from the human pathogenJournal of parasitic diseases : official organ of the Indian Society for Parasitology · 2022Article
- A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions.BMC bioinformatics · 2022Article
- In Silico Methods for Identification of Potential Active Sites of Therapeutic Targets.Molecules (Basel, Switzerland) · 2022Review
- Cloning, Characterization, Expression Analysis, and Agglutination Studies of Novel Gene Encoding β-D-Galactose, N-Acetyl-D-Glucosamine and Lactose-Binding Lectin from Rice Bean (Vigna umbellata).Molecular biotechnology · 2022Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions.Molecules (Basel, Switzerland) · 2021Article
- Finding Druggable Sites in Proteins Using TACTICS.Journal of chemical information and modeling · 2021Article
- MDock: A Suite for Molecular Inverse Docking and Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Inhibitory Potential of Phytochemicals on Interleukin-6-Mediated T-Cell Reduction in COVID-19 Patients: A Computational Approach.Bioinformatics and biology insights · 2021Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods with a Focus on FunFOLD3.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Role of OB-Fold Protein YdeI in Stress Response and Virulence of Salmonella enterica Serovar Enteritidis.Journal of bacteriology · 2020Article
- Diversity-guided Lamarckian random drift particle swarm optimization for flexible ligand docking.BMC bioinformatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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. The GalaxySite web server, freely accessible at http://galaxy.seoklab.org/site, combines such information with molecular docking for more precise binding-site prediction for non-metal ligands. According to the recent critical assessments of structure prediction methods held in 2010 and 2012, this server was found to be superior or comparable to other state-of-the-art programs in the category of ligand-binding-site prediction. A strong merit of the GalaxySite program is that it provides additional predictions on binding ligands and their binding poses in terms of the optimized 3D coordinates of the protein-ligand complexes, whereas other methods predict only identities of binding-site residues or copy binding geometry from similar proteins. The additional information on the specific binding geometry would be very useful for applications in functional studies and computer-aided drug discovery.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.