A5040488997- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- HIV Research and Treatment
- Microbial Metabolic Engineering and Bioproduction
- Immune Cell Function and Interaction
- vaccines and immunoinformatics approaches
- Monoclonal and Polyclonal Antibodies Research
- Microbial Natural Products and Biosynthesis
- Machine Learning in Materials Science
- Click Chemistry and Applications
- Chemical Synthesis and Analysis
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Lung Cancer Treatments and Mutations
- Cancer therapeutics and mechanisms
- Synthesis and biological activity
- Cholinesterase and Neurodegenerative Diseases
- Machine Learning in Bioinformatics
- Mass Spectrometry Techniques and Applications
- Model-Driven Software Engineering Techniques
- PARP inhibition in cancer therapy
- Advanced Proteomics Techniques and Applications
- T-cell and B-cell Immunology
Purdue University West Lafayette
2015-2025
Korea University
2023-2025
Sunchon National University
2019-2024
Seoul National University
2011-2024
Korea Research Institute of Chemical Technology
2024
Duke University
2024
Walter Reed Army Institute of Research
2024
Korea Institute for Advanced Study
2011
Enterovirus D68 (EV-D68) is a member of Picornaviridae and causative agent recent outbreaks respiratory illness in children the United States. We report here crystal structures EV-D68 its complex with pleconaril, capsid-binding compound that had been developed as an anti-rhinovirus drug. The hydrophobic drug-binding pocket viral protein 1 contained density consistent fatty acid about 10 carbon atoms. This could be displaced by pleconaril. also showed pleconaril inhibits at half-maximal...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Knowledge of ligand-binding sites proteins provides invaluable information for functional studies, drug design and protein design. Recent progress in ligand-binding-site prediction methods has demonstrated that using from similar known structures can improve predictions. The GalaxySite web server, freely accessible at http://galaxy.seoklab.org/site, combines such with molecular docking more precise binding-site non-metal ligands. According to the recent critical assessments structure held...
Accurate prediction of the binding affinity a protein-ligand complex is essential for efficient and successful rational drug design. Therefore, many methods have been developed. In recent years, since deep learning technology has become powerful, it also implemented to predict affinity. this work, new neural network model that predicts structure Our using ensemble multiple independently trained networks consist channels 3-D convolutional layers. was 3772 complexes from refined set...
In this article, an enhanced version of GalaxyDock protein–ligand docking program is introduced. performs conformational space annealing (CSA) global optimization to find the optimal binding pose a ligand both in rigid‐receptor mode and flexible‐receptor mode. Binding prediction has been improved compared earlier by efficient generation high‐quality initial conformations for CSA using predocking method based on beta‐complex derived from Voronoi diagram receptor atoms. affinity also...
An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of flexibility using an ensemble precompiled conformations or by employing effectively enlarged binding pocket has been reported be useful. However, direct consideration during energy optimization the docked conformation less popular because large increase computational complexity. In this paper, we present a new program called GalaxyDock that accounts for preselected...
Abstract Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components a successful program an efficient search method and accurate scoring function. In this work, new called LigDockCSA is developed by using powerful global optimization technique, conformational space annealing (CSA), function that combines AutoDock energy piecewise linear potential (PLP) torsion energy. It shown CSA can find lower binding poses than Lamarckian genetic...
We propose a new iterative screening contest method to identify target protein inhibitors. After conducting compound in 2014, we report results acquired from held 2015 this study. Our aims were enzyme inhibitors and benchmark variety of computer-aided drug discovery methods under identical experimental conditions. In both contests, employed the tyrosine-protein kinase Yes as an example protein. Participating groups virtually screened possible library containing 2.4 million compounds....
Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number protein complex structures have been determined using experimental methods, relatively fewer studies performed to determine assembly order complexes. In addition insights into molecular mechanisms function provided by structure a complex, knowing is important for understanding process formation. Assembly also practically useful constructing subcomplexes as step toward solving...
Abstract Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by contest-based approach, in which participants asked to propose prioritized list 400 compounds from designated compound library containing 2.5 million using silico methods and scoring. Our aim was identify enzyme benchmark computer-aided drug discovery under the same experimental conditions. Collecting lists derived various is advantageous for aggregating with structurally...
Virtual screening has become an indispensable procedure in drug discovery. methods can be classified into two categories: ligand-based and structure-based. While the former have advantages, including being quick to compute, general they are relatively weak at discovering novel active compounds because use known actives as references. On other hand, structure-based higher potential find directly predict binding affinity of a ligand target pocket, albeit with substantially lower speed than...
ABSTRACT We report the performance of protein complex prediction approaches our group and their results in CAPRI Rounds 47–55, excluding joint CASP 50 54, as well special COVID‐19 Round 51. Our integrated classical pipelines developed more recently deep learning pipelines. In cases human prediction, we surveyed literature to find information integrate into modeling, such assayed interface residues. addition any information, generated models were selected by a rank aggregation statistical...
We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment PRediction Interactions (CAPRI), an objective assessment modeling. demonstrated noticeable improvement both compared to previous rounds CAPRI, with human predictor group near top rankings server scorer at top. This is first time CAPRI that a has been group. To predict structures, we used multi-chain template-based modeling (TBM) docking program, LZerD. LZerD...