Joo, Keehyoung
Research Professor
Protein structure prediction, Bioinformatics, Artificial Intelligence
I am interested in contributing to the protein structural bioinformatics and their applications based on artificial intelligence (AI) and global optimization. The basic research method employed in AI research is an optimization process for learning models with a large number of parameters, or neural architectures with various network connections. I have been developing computational methodologies to predict the three-dimensional structure of proteins by applying efficient global optimization method. I want to develop AI-based methodologies to protein structure prediction by utilizing global optimization. In the traditional science and engineering field, which solves a given problem through computations and simulations based on human understanding and analysis, AI-based methods show the possibility of overcoming the limitations of conventional methods. I want to make advance the protein structural bioinformatics including protein structure prediction by using artificial intelligence and global optimization. It can be also applied to computational drug discovery.
- B.S. Physics, Sungkyunkwan University, Korea, 1993
- M.A. Physics, Sungkyunkwan University, Korea, 1995
- Ph.D. Physics, Sungkyunkwan University, Korea, 2004
Publications at KIAS
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Molecular mechanism of anion permeation through aquaporin 6
BIOPHYSICAL JOURNAL, 2024 -
DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
BIOINFORMATICS, 2023 -
Application of conformational space annealing to the protein structure modeling using cryo-EM maps
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2023 -
Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome
COMMUNICATIONS BIOLOGY, 2022 -
CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields
MOLECULES, 2022 -
A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2020 -
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2020 -
Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation
SCIENTIFIC REPORTS, 2020 -
Assessment of network module identification across complex diseases
NATURE METHODS, 2019 -
A Mutation in ZNF143 as a Novel Candidate Gene for Endothelial Corneal Dystrophy
JOURNAL OF CLINICAL MEDICINE, 2019 -
ConDo: protein domain boundary prediction using coevolutionary information
BIOINFORMATICS, 2019 -
알파폴드 (AlphaFold): 인공지능 기반 단백질 3차구조 예측
Bio-Technology News (BT News), 2019 -
CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
GLYCOBIOLOGY, 2019 -
Non-sequential protein structure alignment by conformational space annealing and local refinement
PLOS ONE, 2019 -
Morphological Evaluation of Meta-stable Oligomers of alpha-Synuclein with Small-Angle Neutron Scattering
SCIENTIFIC REPORTS, 2018 -
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2018 -
Protein structure modeling and refinement by global optimization in CASP12
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018 -
Data-assisted protein structure modeling by global optimization in CASP12
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018 -
Methods for estimation of model accuracy in CASP12
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2018 -
Conformational Space Annealing explained: A general optimization algorithm, with diverse applications
COMPUTER PHYSICS COMMUNICATIONS, 2018 -
An artificially constructed dimer through deformation of a short zinc-binding loop
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 2018 -
Ergodicity and Model Quality in Template-Restrained Canonical and Temperature/Hamiltonian Replica Exchange Coarse-Grained Molecular Dynamics Simulations of Proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2017 -
Architecture of the type IV coupling protein complex of Legionella pneumophila
NATURE MICROBIOLOGY, 2017 -
Protein Loop Structure Prediction Using Conformational Space Annealing
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2017 -
Contact-assisted protein structure modeling by global optimization in CASP11
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016 -
Template based protein structure modeling by global optimization in CASP11
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016 -
Template-free modeling by LEE and LEER in CASP11
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016 -
Crystal Structure of Hypothetical Fructose-Specific EIIB from Escherichia coli
MOLECULES AND CELLS, 2016 -
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2016 -
Protein structure determination by conformational space annealing using NMR geometric restraints
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2015 -
Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest
BMC BIOINFORMATICS, 2015 -
Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2015 -
The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2015 -
Heterozygous mutations in cyclic AMP phosphodiesterase-4D (PDE4D) and protein kinase A (PKA) provide new insights into the molecular pathology of acrodysostosis
CELLULAR SIGNALLING, 2014 -
Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2014 -
Protein structure modeling for CASP10 by multiple layers of global optimization
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2014 -
Structural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2013 -
Small Heat Shock Protein IbpB Acts as a Robust Chaperone in Living Cells by Hierarchically Activating Its Multi-type Substrate-binding Residues
JOURNAL OF BIOLOGICAL CHEMISTRY, 2013 -
Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2013 -
Sann: Solvent accessibility prediction of proteins by nearest neighbor method
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2012 -
Refinement of protein termini in template-based modeling using conformational space annealing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011 -
Design and efficient production of bovine enterokinase light chain with higher specificity in E. coli
BIOTECHNOLOGY LETTERS, 2011 -
Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening
ENZYME AND MICROBIAL TECHNOLOGY, 2009 -
All-atom chain-building by optimizing MODELLER energy function using conformational space annealing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009 -
Structural Studies of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions
CELL, 2009 -
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009 -
Protein-binding site prediction based on three-dimensional protein modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2009 -
Re-examination of structure optimization of off-lattice protein AB models by conformational space annealing
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2008 -
Multiple Sequence Alignment by Conformational Space Annealing
BIOPHYSICAL JOURNAL, 2008 -
Assessment of predictions submitted for the CASP7 domain prediction category
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007 -
High accuracy template based modeling by global optimization
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007 -
Prediction of the secondary structures of proteins by using PREDICT, a nearest neighbor method on pattern space
JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2004 -
Prediction of protein tertiary structure using PROFESY, a novel method based on fragment assembly and conformational space annealing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2004 -
Profile-based nearest neighbor method for pattern recognition
JOURNAL OF THE KOREAN PHYSICAL SOCIETY, 2004
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