SNU Compbio Lab
Applications
- GalaxySagittarius-AF: Predicting Targets for Drug-Like Compounds in the Extended Human 3D Proteome TOP NEW
- Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction TOP NEW
- Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family TOP NEW
- Benchmarking applicability of medium-resolution cryo-EM protein structures for structure-based drug design TOP NEW
- Atomic-level thermodynamics analysis of the binding free energy of SARS-CoV-2 neutralizing antibodies TOP NEW
Applications and collaborations
- Structural basis of the sweat odorant HMHA recognition by the human odorant receptor OR52E8 TOP NEW
- Structural insights into small-molecule agonist recognition and activation of complement receptor C3aR TOP NEW
- Discovery of highly active kynureninases for cancer immunotherapy through protein language model TOP NEW
- ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation TOP NEW
- Ebastine impairs metastatic spread in triple-negative breast cancer by targeting focal adhesion kinase TOP NEW
- Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling TOP NEW
- Cryo-EM structure of the human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand-binding specificity TOP NEW
- A pGpG-specific phosphodiesterase regulates cyclic di-GMP signaling in Vibrio cholerae TOP NEW
- Structural basis of neuropeptide Y signaling through Y1 receptor TOP NEW
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment TOP NEW
- Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment TOP NEW
- Assessment of protein model structure accuracy estimation in CASP14: Old and new challenges TOP NEW
- Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies TOP NEW
- Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth TOP NEW
- Symmetry-related residues as promising hotspots for the evolution of de novo oligomeric enzymes TOP NEW
- Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane TOP NEW
- Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains TOP NEW
- Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane TOP NEW
- Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling TOP NEW
- Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment TOP NEW
- Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning TOP NEW
- Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease TOP NEW
- Structural Basis for the Enantioselectivity of Esterase Est-Y29 toward (S)-Ketoprofen TOP NEW
- Biophysical and functional characterization of Norrin signaling through Frizzled4 TOP NEW
- An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 TOP NEW
- The challenge of modeling protein assemblies: the CASP12-CAPRI experiment TOP NEW
- Cell–cell adhesion in metazoans relies on evolutionarily conserved features of the α-catenin·β-catenin–binding interface TOP NEW
- Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4 TOP NEW
- Absolute binding free energies for octa-acids and guests in SAMPL5 TOP NEW
- Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge TOP NEW
- Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment TOP NEW
- Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System TOP NEW
- Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds TOP NEW
- Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues TOP NEW
- Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy TOP NEW
- Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif TOP NEW
- Blind prediction of interfacial water positions in CAPRI TOP NEW
- Community-wide evaluation of methods for predicting the effect of mutations on protein–protein interactions TOP NEW
- New molecular interaction of IIANtr and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies TOP NEW
- Switchable Nanoporous Sheets by the Aqueous Self-Assembly of Aromatic Macrobicycles TOP NEW
- What stabilizes close arginine pairing in proteins? TOP NEW
- Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA TOP NEW
- Pulsating Tubules from Noncovalent Macrocycles TOP NEW
- Discovery, design and synthesis of Y-shaped peroxisome proliferator-activated receptor δ agonists as potent anti-obesity agents in vivo TOP NEW
- Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology TOP NEW
- How Does a Registry Change in Dynein’s Coiled-Coil Stalk Drive Binding of Dynein to Microtubules? TOP NEW
- De novo protein structure prediction by dynamic fragment assembly and conformational space annealing TOP NEW
- Transmembrane Signaling of Chemotaxis Receptor Tar: Insights from Molecular Dynamics Simulation Studies TOP NEW
- Self-Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles TOP NEW
- Transition between B-DNA and Z-DNA: Free Energy Landscape for the B−Z Junction Propagation TOP NEW
- Structural Basis of Functional Conversion of a Floral Repressor to an Activator: A Molecular Dynamics Simulation Study TOP NEW
- Cooperativity and Specificity of Cys2His2 Zinc Finger Protein-DNA Interactions: A Molecular Dynamics Simulation Study TOP NEW
- Strength of Cα−H···O=C Hydrogen Bonds in Transmembrane Proteins TOP NEW
- Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations TOP NEW
Prediction of protein-ligand interactions
- G-screen: Scalable Receptor-Aware Virtual Screening through Flexible Ligand Alignment TOP NEW
- Physics-Inspired Accuracy Estimator for Model-Docked Ligand Complexes TOP NEW
- CSearch: chemical space search via virtual synthesis and global optimization TOP NEW
- GalaxyDock-DL: Protein-Ligand Docking by Global Optimization and Neural Network Energy TOP NEW
- CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking TOP NEW
- GalaxyDock2-HEME: protein-ligand docking for heme proteins TOP NEW
- HProteome-BSite: predicted binding sites and ligands in human 3D proteome TOP NEW
- GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network TOP NEW
- GalaxyWater-wKGB: Prediction of Water Positions on Protein Structure Using wKGB Statistical Potential TOP NEW
- GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein Targets for Druglike Compounds TOP NEW
- GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility TOP NEW
- GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking TOP NEW
- Galaxy7TM: Flexible GPCR-ligand docking by structure refinement TOP NEW
- Evaluation of GalaxyDock Based on the Community Structure–Activity Resource 2013 and 2014 Benchmark Studies TOP NEW
- GalaxySite: ligand-binding-site prediction by using molecular docking TOP NEW
- GalaxyDock2: Protein–ligand docking using beta-complex and global optimization TOP NEW
- GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains TOP NEW
- Conformational Sampling of Flexible Ligand-binding Protein Loops TOP NEW
- LigDockCSA: Protein–ligand docking using conformational space annealing TOP NEW
- A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect TOP NEW
Prediction of protein-protein interactions
- GalaxyDomDock: An ab initio domain–domain docking web server for multi-domain protein structure prediction TOP NEW
- GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking TOP NEW
- GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters TOP NEW
- GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure TOP NEW
- GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking TOP NEW
- GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity TOP NEW
Protein structure prediction
- Protein Loop Structure Prediction by Community-based Deep Learning and its Application to Antibody CDR H3 Loop Modeling TOP NEW
- Protein oligomer structure prediction using GALAXY in CASP14 TOP NEW
- Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45 TOP NEW
- Prediction of protein oligomer structures using GALAXY in CASP13 TOP NEW
- GalaxyRefine2: Simultaneous refinement of inaccurate local regions and overall protein structure TOP NEW
- GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors TOP NEW
- Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment TOP NEW
- Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30 TOP NEW
- Effective protein model structure refinement by loop modeling and overall relaxation TOP NEW
- Galaxy7TM: Flexible GPCR-ligand docking by structure refinement TOP NEW
- Protein Loop Modeling Using a New Hybrid Energy Function and Its Application to Modeling in Inaccurate Structural Environments TOP NEW
- GalaxyRefine: protein structure refinement driven by side-chain repacking TOP NEW
- GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions TOP NEW
- Refinement of unreliable local regions in template-based protein models TOP NEW
- GalaxyWEB server for protein structure prediction and refinement TOP NEW
- Refinement of protein termini in template-based modeling using conformational space annealing TOP NEW
- The FALC-Loop web server for protein loop modeling TOP NEW
- Protein loop modeling by using fragment assembly and analytical loop closure TOP NEW
- Protein Loop Modeling Using Fragment Assembly TOP NEW
- Resultants and loop closure TOP NEW
- Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller TOP NEW
- The flexibility in the proline ring couples to the protein backbone TOP NEW
- Using quaternions to calculate RMSD TOP NEW
- A kinematic view of loop closure TOP NEW
Reviews and methods
- Artificial Intelligence in Therapeutic Antibody Design: Advances and Future Prospects TOP NEW
- Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server. In "Protein Structure Prediction" TOP NEW
- Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock. In "Modeling Peptide-Protein Interactions" TOP NEW
- Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers. In "Computational Design of Ligand Binding Proteins" TOP NEW
- High-resolution protein–protein docking by global optimization: recent advances and future challenges TOP NEW
- Prediction of Protein Structure and Interaction by GALAXY Protein Modeling Programs TOP NEW
others
Benchmark
Immunogenicity prediction
Miscellaneous
- A benchmark study of machine learning methods for molecular electronic transition: Tree-based ensemble learning versus graph neural network TOP NEW
- MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization TOP NEW
- Accurate protein structure prediction: what comes next? TOP NEW
- Tribute to Ken A. Dill TOP NEW
- Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors TOP NEW
- Efficiency of Rotational Operators for Geometric Manipulation of Chain Molecules TOP NEW
- Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces TOP NEW
Prediction of molecular properties by machine learning
Prediction of protein ligand interaction
- MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change TOP NEW
- GalaxyCDock: Webserver for Covalent Protein–Ligand Binding Mode Prediction TOP NEW
Prediction of protein-peptide interactions
- Deep learning molecular interaction motifs from Receptor structure alone TOP NEW
- GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization TOP NEW