• Clinical and Experimental Vaccine Research
• /
• v.13 no.3
• /
• pp.202-217
• /
• 2024

Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.

• Journal of Preventive Medicine and Public Health
• /
• v.42 no.6
• /
• pp.343-348
• /
• 2009

The final decision of study design in molecular and genetic epidemiology is usually a compromise between the research study aims and a number of logistical and ethical barriers that may limit the feasibility of the study or the interpretation of results. Although biomarker measurements may improve exposure or disease assessments, it is necessary to address the possibility that biomarker measurement inserts additional sources of misclassification and confounding that may lead to inconsistencies across the research literature. Studies targeting multi-causal diseases and investigating gene-environment interactions must not only meet the needs of a traditional epidemiologic study but also the needs of the biomarker investigation. This paper is intended to highlight the major issues that need to be considered when developing an epidemiologic study utilizing biomarkers. These issues covers from molecular and genetic epidemiology (MGE) study designs including cross-sectional, cohort, case-control, clinical trials, nested case-control, and case-only studies to matching the study design to the MGE research goals. This review summarizes logistical barriers and the most common epidemiological study designs most relevant to MGE and describes the strengths and limitations of each approach in the context of common MGE research aims to meet specific MEG objectives.

• Journal of Photoscience
• /
• v.10 no.3
• /
• pp.251-255
• /
• 2003

The composites fabricated by blending nonlinear optical (NLO) chromophore such as {4-[2-(4-nitrophenyl)-vinyl] phenyl}diphenylamine (NVPDA) with photoconducting crosslinkable matrix, bis-(4-ethynylphenyl)-(4-octyloxy-phenyl)amine (BEOPEA), showed photorefractive property. Many problems faced in typical organic photorefractive systems such as time-consuming chemical synthesis, difficulty in rational design, intrinsic instability and phase separation could be avoided by this fabrication method.

• BMB Reports
• /
• v.41 no.6
• /
• pp.444-447
• /
• 2008

Trypanothione reductase is an important target enzyme for structure-based drug design against Leishmania. We used homology modeling to construct a three-dimensional structure of the trypanothione reductase (TR) of Leishmania infantum. The structure shows acceptable Ramachandran statistics and a remarkably different active site from glutathione reductase(GR). Thus, a specific inhibitor against TR can be designed without interfering with host (human) GR activity.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.10
• /
• pp.1495-1498
• /
• 2004

A novel-type of structurally simple fluorescent chemosensor for oxalic acid was designed, synthesized, and evaluated to show that it detects oxalic acid in methanol with high selectivity over other anions including monoand dibasic carboxylic acids.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.08a
• /
• pp.205-205
• /
• 2011

The self-assembly of ${\gamma}$-phenylalanine on Au(111) at 150 K was investigated using scanning tunneling microscopy (STM). Phenylalanine can potentially form two-dimensional (2D) molecular networks through hydrogen bonding (through the carboxyl and amino groups) and ${\pi}-{\pi}$ stacking interactions (via aromatic rings). We found that ${\gamma}$-phenylalanine molecules self-assembled on Au(111) surfaces into well-ordered structures such as ring-shaped clusters (at low and intermediate coverages) and 2D molecular domains (intermediate and monolayer coverages), whereas ${\alpha}$-phenylalanine molecules formed less-ordered structure on Au(111). The self-assembly of ${\gamma}$- but not ${\alpha}$-phenylalanine may be related to the flexibility of the carboxyl and amino groups in the molecule. Moreover, as expected, the 2D molecular network of ${\gamma}$-phenylalanine on Au(111) was mediated by a combination of hydrogen bonding and ${\pi}-{\pi}$ stacking interactions.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.2
• /
• pp.613-619
• /
• 2012

We applied several machine learning methods for developing QSAR models for prediction of acute toxicity to fathead minnow. The multiple linear regression (MLR) and artificial neural network (ANN) method were applied to predict 96 h $LC_{50}$ (median lethal concentration) of 555 chemical compounds. Molecular descriptors based on 2D chemical structure were calculated by PreADMET program. The recursive partitioning (RP) model was used for grouping of mode of actions as reactive or narcosis, followed by MLR method of chemicals within the same mode of action. The MLR, ANN, and two RP-MLR models possessed correlation coefficients ($R^2$) as 0.553, 0.618, 0.632, and 0.605 on test set, respectively. The consensus model of ANN and two RP-MLR models was used as the best model on training set and showed good predictivity ($R^2$=0.663) on the test set.

• Journal of Mechanical Science and Technology
• /
• v.18 no.11
• /
• pp.2042-2048
• /
• 2004

A molecular dynamics study has been conducted on an external-force-field-induced isothermal crystallization process of amorphous structures as a new low-temperature athermal crystallization process. An external cyclic-force field with a dc bias is imposed on molecules selected randomly in an amorphous-phase of argon. Multiple peaks smoothed out in the radial distribution functions for amorphous states appear very clearly during the crystallization process that cannot be achieved otherwise. When the amorphous material is locally exposed to an external force field, crystallization starts and propagates from the interfacial region and crystallization growth rates can be estimated.

• Toxicological Research
• /
• v.17
• /
• pp.205-210
• /
• 2001

One of the major focuses and perhaps the greatest challenges during the past decade in the discipline of immunotoxicology has been the elucidation of the molecular mechanisms responsible for immunotoxicity by specific agents. Much is currently understood about the basic underlying intracellular processes that control leukocyte effector function. This fundamental information in cell biology can now be applied toward developing systematic approaches, through the application of cell and molecular biology techniques, to identify the intracellular targets and processes disrupted by immunotoxicants. The objective of this paper is two fold. First to discuss fundamental principles of experimental design aimed at elucidation of cellular mechanisms in immunotoxicology; and second to discuss the application of molecular biology techniques in characterizing the mechanism of TCDD-induced B cell dysfunction as a working example.

• Journal of Integrative Natural Science
• /
• v.6 no.3
• /
• pp.138-142
• /
• 2013

The HIV-1 envelope glycoprotein gp120 plays a vital role in the entry of the virus into the host cells. The crucial role of the glycoprotein suggests gp120 as potential drug target for the future antiviral therapies. Identification of the binding mode of small drug like compounds has been an important goal in drug design. In the current study we attempt to propose binding mode of indole derivatives in the binding pocket of gp120. These derivatives are reported to inhibit HIV-1 by acting as attachment inhibitors that bind to gp120 and prevent the gp120-CD4 interaction and thus inhibit the infectivity of HIV-1. To elucidate the molecular basis of the small molecules interactions to inhibit the glycoprotein function we employed the molecular docking simulation approach. This study provides insights to elucidate the binding pattern of indole-based gp120 inhibitors and may help in the rational design of novel HIV-1 inhibitors with improved potency.