ArticleProtein science : a publication of the Protein Society2016
G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.
Article in Protein science : a publication of the Protein Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites.Scientific reports · 2024Article
- CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein-Ligand Binding Modes.Journal of chemical information and modeling · 2023Article
- HLA-Clus: HLA class I clustering based on 3D structure.BMC bioinformatics · 2023Article
- Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase.Current research in structural biology · 2023Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- GraphSite: Ligand Binding Site Classification with Deep Graph Learning.Biomolecules · 2022Article
- SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites.PLoS computational biology · 2022Article
- A New Strategy for Multitarget Drug Discovery/Repositioning Through the Identification of Similar 3D Amino Acid Patterns Among Proteins Structures: The Case of Tafluprost and its Effects on Cardiac Ion Channels.Frontiers in pharmacology · 2022Article
- Unexpected similarity between HIV-1 reverse transcriptase and tumor necrosis factor binding sites revealed by computer vision.Journal of cheminformatics · 2021Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- CHARMM-GUIJournal of chemical information and modeling · 2021Article
- Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures.Journal of chemical information and modeling · 2021Article
- BionoiNet: ligand-binding site classification with off-the-shelf deep neural network.Bioinformatics (Oxford, England) · 2020Article
- Improving detection of protein-ligand binding sites with 3D segmentation.Scientific reports · 2020Article
- Ligand-Binding-Site Structure Refinement Using Molecular Dynamics with Restraints Derived from Predicted Binding Site Templates.Journal of chemical theory and computation · 2019Article
- Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases.Briefings in bioinformatics · 2019Review
- Stalis: A Computational Method for Template-Based Ab Initio Ligand Design.Journal of computational chemistry · 2019Article
- Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing.Journal of molecular biology · 2019Article
- DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network.PLoS computational biology · 2019Article
- Prediction Methods of Herbal Compounds in Chinese Medicinal Herbs.Molecules (Basel, Switzerland) · 2018Review
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2 authors.
Funding
Abstract
Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.
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