List of works - Chaok Seok

A benchmark study of machine learning methods for molecular electronic transition: Tree‐based ensemble learning versus graph neural network

scientific article published in 2022

A kinematic view of loop closure

scientific article

A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.

scientific article

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

scientific article published on 30 September 2016

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

scientific article published on 27 September 2016

Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling

scientific article published on 10 June 2020

Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

scientific article published on 17 June 2013

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

scientific article

Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces

scientific article published in April 2004

Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges

article published in 2021

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning

scientific article published on 30 August 2019

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

scientific article published on 29 March 2017

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.

scientific article

Biophysical and functional characterization of Norrin signaling through Frizzled4

scientific article published on 13 August 2018

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study

scientific article published in June 2010

Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System

scientific article

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

scientific article

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

scientific article published on 19 June 2020

Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth

scientific article published on 06 September 2021

Discovery, design and synthesis of Y-shaped peroxisome proliferator-activated receptor δ agonists as potent anti-obesity agents in vivo.

scientific article published on 6 April 2012

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

scientific article published on 16 September 2021

Effective protein model structure refinement by loop modeling and overall relaxation

scientific article

Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies

scientific article

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds

scientific article

Galaxy7TM: flexible GPCR-ligand docking by structure refinement

scientific article published on 29 April 2016

GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

scientific article published on 16 June 2017

GalaxyDock2: protein-ligand docking using beta-complex and global optimization

scientific article

GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility

scientific article published on 19 August 2019

GalaxyDock: protein-ligand docking with flexible protein side-chains

scientific article published on 12 December 2012

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors

scientific article published on 07 June 2018

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

scientific article published on 14 February 2013

GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking

scientific article published on 01 July 2021

GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure

scientific article

GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization

scientific article published on 12 May 2015

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

scientific article published on 01 July 2019

GalaxyRefine: Protein structure refinement driven by side-chain repacking

scientific article

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

scientific article published on 18 August 2016

GalaxySagittarius: Structure- and similarity-based prediction of protein targets for drug-like compounds

scientific article published on 13 May 2020

GalaxySite: ligand-binding-site prediction by using molecular docking

scientific article

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

scientific article

GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters

scientific article published on 07 June 2019

GalaxyWEB server for protein structure prediction and refinement

scientific article

High-resolution protein-protein docking by global optimization: recent advances and future challenges

scientific article published on 18 August 2015

How does a registry change in dynein's coiled-coil stalk drive binding of dynein to microtubules?

scientific article published on 10 August 2011

LigDockCSA: protein-ligand docking using conformational space annealing.

scientific article published on 12 August 2011

MOPED: method for optimizing physical energy parameters using decoys.

scientific article published in January 2003

Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues.

scientific article published on 29 May 2015

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

scientific article published on 01 January 2020

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

scientific article published on 21 May 2020

New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

scientific article

Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease

scientific article published on 01 February 2019

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

scientific article

Prediction of Molecular Electronic Transitions Using Random Forests

scientific article published on 22 October 2020

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Prediction of protein oligomer structures using GALAXY in CASP13

scientific article published on 09 October 2019

Protein loop modeling by using fragment assembly and analytical loop closure

scientific article

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

scientific article

Pulsating tubules from noncovalent macrocycles

scientific article published in September 2012

Refinement of protein termini in template-based modeling using conformational space annealing

scientific article published on 13 July 2011

Refinement of unreliable local regions in template-based protein models

scientific article

Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller

scientific article

Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains

scientific article published on 23 October 2020

Self‐Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles ⬇️

scientific article published on November 2, 2010

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

scientific article published on 16 October 2017

Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins

scientific article published on 22 December 2007

Structural and functional characterization of the α-catenin·β-catenin binding interface in Caenorhabditis elegans reveals conserved requirements for cell-cell adhesion in metazoans.

scientific article published on 25 August 2017

Structural basis of neuropeptide Y signaling through Y1 receptor

scientific article published on 14 February 2022

Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif

scientific article

Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45

scientific article published on 27 November 2019

Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane

scientific article

Switchable nanoporous sheets by the aqueous self-assembly of aromatic macrobicycles

scientific article published on 6 May 2013

Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock

scientific article

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

scientific article published on 22 October 2016

The FALC-Loop web server for protein loop modeling

scientific article

The challenge of modeling protein assemblies: The CASP12-CAPRI experiment.

scientific article published on 10 November 2017

The flexibility in the proline ring couples to the protein backbone

scientific article

Transition between B-DNA and Z-DNA: free energy landscape for the B-Z junction propagation

scientific article published in August 2010

Transmembrane signaling of chemotaxis receptor tar: insights from molecular dynamics simulation studies

scientific article

Tribute to Ken A. Dill

scientific article published on 01 May 2018

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

scientific article published in January 2007

Using quaternions to calculate RMSD

scientific article

What stabilizes close arginine pairing in proteins?

scientific article

List of works by Chaok Seok

A benchmark study of machine learning methods for molecular electronic transition: Tree‐based ensemble learning versus graph neural network

A kinematic view of loop closure

A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect.

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Aldehyde-alcohol dehydrogenase undergoes structural transition to form extended spirosomes for substrate channeling

Alternative zinc-binding sites explain the redox sensitivity of zinc-containing anti-sigma factors

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Analytic density-functional self-consistent-field theory of diblock copolymers near patterned surfaces

Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.

Biophysical and functional characterization of Norrin signaling through Frizzled4

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study

Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing

Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane

Discovery of a transdermally deliverable pentapeptide for activating AdipoR1 to promote hair growth

Discovery, design and synthesis of Y-shaped peroxisome proliferator-activated receptor δ agonists as potent anti-obesity agents in vivo.

Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies

Effective protein model structure refinement by loop modeling and overall relaxation

Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds

Galaxy7TM: flexible GPCR-ligand docking by structure refinement

GalaxyDock BP2 score: a hybrid scoring function for accurate protein-ligand docking

GalaxyDock2: protein-ligand docking using beta-complex and global optimization

GalaxyDock3: Protein-ligand docking that considers the full ligand conformational flexibility

GalaxyDock: protein-ligand docking with flexible protein side-chains

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

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

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

GalaxyRefine: Protein structure refinement driven by side-chain repacking

GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking

GalaxySagittarius: Structure- and similarity-based prediction of protein targets for drug-like compounds

GalaxySite: ligand-binding-site prediction by using molecular docking

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions

GalaxyTongDock: Symmetric and asymmetric ab initio protein-protein docking web server with improved energy parameters

GalaxyWEB server for protein structure prediction and refinement

High-resolution protein-protein docking by global optimization: recent advances and future challenges

How does a registry change in dynein's coiled-coil stalk drive binding of dynein to microtubules?

LigDockCSA: protein-ligand docking using conformational space annealing.

MOPED: method for optimizing physical energy parameters using decoys.

Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues.

Modeling Protein Homo-Oligomer Structures with GalaxyHomomer Web Server

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies

Novel Compound Heterozygote Mutation in IL10RA in a Patient With Very Early-Onset Inflammatory Bowel Disease

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy

Prediction of Molecular Electronic Transitions Using Random Forests

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Prediction of protein oligomer structures using GALAXY in CASP13

Protein loop modeling by using fragment assembly and analytical loop closure

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

Pulsating tubules from noncovalent macrocycles

Refinement of protein termini in template-based modeling using conformational space annealing

Refinement of unreliable local regions in template-based protein models

Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller

Sclerostin inhibits Wnt signaling through tandem interaction with two LRP6 ectodomains

Self‐Dissociating Tubules from Helical Stacking of Noncovalent Macrocycles ⬇️

Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment

Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins

Structural and functional characterization of the α-catenin·β-catenin binding interface in Caenorhabditis elegans reveals conserved requirements for cell-cell adhesion in metazoans.

Structural basis of neuropeptide Y signaling through Y1 receptor

Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif

Structure prediction of biological assemblies using GALAXY in CAPRI rounds 38-45

Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane

Switchable nanoporous sheets by the aqueous self-assembly of aromatic macrobicycles

Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

The FALC-Loop web server for protein loop modeling