Search Results - "PAK, Youngshang"

Computational study of the pKa values of a modified G·C base pair in duplex DNA by Kim, Hyeonjun, Pak, Youngshang

“…During the demethylation of 5‐methyl cytosine residues in duplex DNAs, formyl or carboxyl cytosines are produced and these modified cytosines are…”
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Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field by Yang, Changwon, Lim, Manho, Kim, Eunae, Pak, Youngshang

“…We proposed a simple van der Waals backbone correction (O2′ and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal…”
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Conformer-Specific Photodissociation Dynamics of CF2ICF2I in Solution Probed by Time-Resolved Infrared Spectroscopy by Park, Seongchul, Lee, Taegon, Shin, Juhyang, Yoon, Hojeong, Pak, Youngshang, Lim, Manho

“…The photodissociation dynamics of CF2ICF2I in solution was investigated from 0.3 ps to 100 μs, after the excitation of CF2ICF2I with a femtosecond UV pulse…”
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Effect of antigen shedding on targeted delivery of immunotoxins in solid tumors from a mathematical model by Pak, Youngshang, Pastan, Ira, Kreitman, Robert J, Lee, Byungkook

“…Most cancer-specific antigens used as targets of antibody-drug conjugates and immunotoxins are shed from the cell surface (Zhang & Pastan (2008) Clin. Cancer…”
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Large Tunneling Effect on the Hydrogen Transfer in Bis(μ-oxo)dicopper Enzyme: A Theoretical Study by Park, Kisoo, Pak, Youngshang, Kim, Yongho

“…Type-III copper-containing enzymes have dicopper centers in their active sites and exhibit a novel capacity for activating aliphatic C–H bonds in various…”
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Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment by Kim, Eunae, Yang, Changwon, Pak, Youngshang

“…Thrombin-binding aptamer (TBA-15) is a single-stranded 15-mer oligonucleotide that has a wide range of biomedical applications. In the presence of metal…”
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Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations by Jang, Soonmin, Kim, Eunae, Shin, Seokmin, Pak, Youngshang

“…We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the…”
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Replica-exchange method using the generalized effective potential by Jang, Soonmin, Shin, Seokmin, Pak, Youngshang

“…We propose an effective scheme for fast conformational searches by combining the replica exchange method (REM) with the generalized effect potential concept…”
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Relationship between the Ratio of Ligand to Metal and the Coordinating Ability of Anions. Synthesis and Structural Properties of AgX-Bearing Bis(4-pyridyl)dimethylsilane (X- = NO2 -, NO3 -, CF3SO3 -, and PF6 -) by Lee, Jung Woon, Kim, Eun Ae, Kim, Yun Ju, Lee, Young-A, Pak, Youngshang, Jung, Ok-Sang

“…Studies of the anion effects on the molecular construction of a series of AgX complexes with bis(4-pyridyl)dimethylsilane (L) (X- = NO2 -, NO3 -, CF3SO3 -, and…”
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Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA by Kim, Hyeonjun, Pak, Youngshang

“…The A:8OG base pair (bp) is the outcome of DNA replication of the mismatched C:8OG bp. A high A:8OG bp population increases the C/G to A/T transversion…”
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Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level by Kim, Hyeonjun, Pak, Youngshang

“…DNA glycosylases play key roles in the maintenance of genomic integrity. These enzymes effectively find rare damaged sites in DNA and participate in subsequent…”
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Improving All-Atom Force Field to Accurately Describe DNA G‑Quadruplex Loops by Kim, Hyeonjun, Pak, Youngshang

“…The DNA G-quadruplex (GQ) displays structural polymorphisms, and interactions between its loops and flanking sequences critically determine which of the…”
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Computational study of the pK a values of a modified G·C base pair in duplex DNA by Kim, Hyeonjun, Pak, Youngshang

“…Abstract During the demethylation of 5‐methyl cytosine residues in duplex DNAs, formyl or carboxyl cytosines are produced and these modified cytosines are…”
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Computational Probing of the Folding Mechanism of Human Telomeric G‑Quadruplex DNA by Kim, Hyeonjun, Kim, Eunae, Pak, Youngshang

“…The human telomeric (htel) sequences in the terminal regions of human telomeres form diverse G-quadruplex (GQ) structures. Despite much experimental efforts to…”
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Computational Probing of Temperature-Dependent Unfolding of a Small Globular Protein: From Cold to Heat Denaturation by Yang, Changwon, Jang, Soonmin, Pak, Youngshang

“…Fully atomistic replica exchange molecular dynamics simulations are performed to compute the stability curve of a small globular protein as accurately as…”
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A fully atomistic computer simulation study of cold denaturation of a β-hairpin by Yang, Changwon, Jang, Soonmin, Pak, Youngshang

“…Cold denaturation is a fundamental phenomenon in aqueous solutions where the native structure of proteins disrupts on cooling. Understanding this process in…”
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Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA by Yang, Changwon, Kim, Eunae, Pak, Youngshang

“…Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC)…”
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In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level by Yang, Changwon, Kulkarni, Mandar, Lim, Manho, Pak, Youngshang

“…The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged…”
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Free-Energy Landscape of a pH-Modulated G·C Base Pair Transition from Watson–Crick to Hoogsteen State in Duplex DNA by Kim, Hyeonjun, Yang, Changwon, Pak, Youngshang

“…In double-helical DNAs, the most stable Watson–Crick (WC) base pair (bp) can be in thermal equilibrium with much less abundant Hoogsteen (HG) bp by the…”
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Improving Temperature Generator in Parallel Tempering Simulation in the NPT Condition by Yang, Changwon, Kim, Hyeonjun, Pak, Youngshang

“…Parallel tempering (PT) simulations provide a powerful computational tool to accelerate conformational searches of complex molecular systems. In this method,…”
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