PKCι Is a Promising Target Suppressing UVB-Induced MMP- 1 Expression by 7,8,4’-Trihydroxyisoflavone

Juyong Kim,Younghyun Lee,Jong-Eun Kim,Sohee Baek,Charles C. Lee,Ki Won Lee,Jun Seong Park,Deok-kun Oh,Zigang Dong,Chang Yong Lee,Ann M Bode,Hanyong Chen 한국식품영양과학회 2014 한국식품영양과학회 학술대회발표집 Vol.2014 No.10

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

Lee, Juyong,Lee, Kiho,Joung, InSuk,Joo, Keehyoung,Brooks, Bernard R,Lee, Jooyoung BioMed Central 2015 BMC bioinformatics Vol.16 No.-

<P><B>Background</B></P><P>In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaussian distribution, the variability of a spatial restraint, is closely related to the reliability of the restraint information extracted from a template, and it should be accurately estimated for successful template-based protein structure modeling.</P><P><B>Results</B></P><P>To predict the variability of the spatial restraints in template-based modeling, we have devised a prediction model, Sigma-RF, by using the random forest (RF) algorithm. The benchmark results on 22 CASP9 targets show that the variability values from Sigma-RF are of higher correlations with the true distance deviation than those from Modeller. We assessed the effect of new sigma values by performing the single-domain homology modeling of 22 CASP9 targets and 24 CASP10 targets. For most of the targets tested, we could obtain more accurate 3D models from the identical alignments by using the Sigma-RF results than by using Modeller ones.</P><P><B>Conclusions</B></P><P>We find that the average alignment quality of residues located between and at two aligned residues, quasi-local information, is the most contributing factor, by investigating the importance of input features used in the RF machine learning. This average alignment quality is shown to be more important than the previously identified quantity of a local information: the product of alignment qualities at two aligned residues.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-015-0526-z) contains supplementary material, which is available to authorized users.</P>

<i>De novo</i> protein structure prediction by dynamic fragment assembly and conformational space annealing

Lee, Juyong,Lee, Jinhyuk,Sasaki, Takeshi N.,Sasai, Masaki,Seok, Chaok,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2011 Proteins Vol.79 No.8

<P><B>Abstract</B></P><P><I>Ab initio</I> protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an <I>ab initio</I> structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short‐ and long‐range structural restraint information from a fragment library. Here, DFA is represented by the full‐atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single‐domain proteins and 13 template‐free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Proteins 2011; © 2011 Wiley‐Liss, Inc.</P>

RetroTRAE: Retrosynthetic Translation of \\ Atomic Environments with Transformer

Juyong Lee(이주용),Umit V. Ucak,Islambek Ashyrmamatov,Junsu Ko 한국고분자학회 2022 한국고분자학회 학술대회 연구논문 초록집 Vol.47 No.1

Combination Analysis and Switching Method of a Cascaded H-Bridge Multilevel Inverter Based on Transformers With the Different Turns Ratio for Increasing the Voltage Level

Lee, June-Seok,Sim, Hyun-Woo,Kim, Juyong,Lee, Kyo-Beum Institute of Electrical and Electronics Engineers 2018 IEEE transactions on industrial electronics Vol.65 No.6

<P>This paper analyzes the combination in a cascaded H-bridge multilevel inverter (CHBI) based on transformers with the different turn ratios for increasing the voltage level and proposes the switching method for achieving the output voltage distribution among H-bridge cells (HBCs). The transformers used in this paper are connected to the output of the respective HBCs, and the secondary sides of all the transformers are connected in series for generating the final output voltage. Only one of the transformers, in particular, has a different turn ratio for increasing the output voltage level. In this paper, the possible turn ratio of the special transformer with a different turn ratio is discussed in detail, and a switching method based on the level-shifted switching method for the topology used in this paper is proposed. To verify the effectiveness of the proposed method, a three-phase 21-level CHBI is experimentally tested.</P>

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

Lee, Juyong,Tofoleanu, Florentina,Pickard IV, Frank C.,Kö,nig, Gerhard,Huang, Jing,Damjanović,, Ana,Baek, Minkyung,Seok, Chaok,Brooks, Bernard R. Springer-Verlag 2017 Journal of computer-aided molecular design Vol.31 No.1

<P>Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett's acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments.</P>

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

Lee, Juyong,Seok, Chaok Wiley Subscription Services, Inc., A Wiley Company 2008 Proteins Vol.70 No.3

<P>Computational prediction of protein–ligand binding modes provides useful information on the relationship between structure and activity needed for drug design. A statistical rescoring method that incorporates entropic effect is proposed to improve the accuracy of binding mode prediction. A probability function for two sampled conformations to belong to the same broad basin in the potential energy surface is introduced to estimate the contribution of the state represented by a sampled conformation to the configurational integral. The rescoring function is reduced to the colony energy introduced by Xiang et al. (Proc Natl Acad Sci USA 2002;99:7432–7437) when a particular functional form for the probability function is used. The scheme is applied to rescore protein–ligand complex conformations generated by AutoDock. It is demonstrated that this simple rescoring improves prediction accuracy substantially when tested on 163 protein–ligand complexes with known experimental structures. For example, the percentage of complexes for which predicted ligand conformations are within 1 Å root-mean-square deviation from the native conformations is doubled from about 20% to more than 40%. Rescoring with 11 different scoring functions including AutoDock scoring functions were also tested using the ensemble of conformations generated by Wang et al. (J Med Chem 2003;46:2287–2303). Comparison with other methods that use clustering and estimation of conformational entropy is provided. Examination of the docked poses reveals that the rescoring corrects the predictions in which ligands are tightly fit into the binding pockets and have low energies, but have too little room for conformational freedom and thus have low entropy. Proteins 2008. © 2007 Wiley-Liss, Inc.</P>

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

Lee, Juyong,Joo, Keehyoung,Brooks, Bernard R.,Lee, Jooyoung American Chemical Society 2015 Journal of chemical theory and computation Vol.11 No.7

<P>We present a new all-atom structure-based method to study protein conformational transitions using Lorentzian attractive interactions based on native structures. The variability of each native contact is estimated based on evolutionary information using a machine learning method. To test the validity of this approach, we have investigated the conformational transition of adenylate kinase (ADK). The intrinsic boundedness of the Lorentzian attractive interactions facilitated frequent conformational transitions, and consequently we were able to observe more than 1000 structural interconversions between the open and closed states of ADK out of a total of 6 μs MD simulations. ADK has three domains: the nucleoside monophosphate (NMP) binding domain, the LID-domain, and the CORE domain, which catalyze the interconversion between ATP and ADP. We identified two transition states: a more frequent LID-closed-NMP-open (TS1) state and a less frequent LID-open-NMP-closed (TS2) state. The transition was found to be symmetric in both directions via TS1. We also obtained an off-pathway metastable state that was previously observed with physics-based all-atom simulations but not with coarse-grained models. In the metastable state, the LID domain was slightly twisted and formed contacts with the NMP domain. Our model correctly identified a total of 14 out of the top 16 residues with highest fluctuation by NMR experiment, thus showing excellent agreement with experimental NMR relaxation data and overwhelmingly better results than existing models.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2015/jctcce.2015.11.issue-7/acs.jctc.5b00268/production/images/medium/ct-2015-002683_0011.gif'></P>

Contribution of Counterion Entropy to the Salt-Induced Transition Between B-DNA and Z-DNA

Lee, Youn-Kyoung,Lee, Juyong,Choi, Jung Hyun,Seok, Chaok Korean Chemical Society 2012 Bulletin of the Korean Chemical Society Vol.33 No.11

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

Quantification of Lard In Animal Fat Product With Simple Calculation From Raman Spectroscopy

Juyong LEE,Jinho PARK,Hyoyoung MUN,Min-Gon KIM 한국생물공학회 2017 한국생물공학회 학술대회 Vol.2017 No.4