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