Computational Biochemistry
Computational Biochemistry Read More »
Classes
Posts related to the classes by Prof. Seungpyo Hong in Jeonbuk National University (JBNU)
Lecture materials will be provided in this category. You need to log in the site for full access of the contents. The students enrolled in classes taught by Prof. Seungpyo Hong will be granted access to the posts.
Molecular Dynamics Simulation
Introduction Molecular dynamics (MD) simulation is a computational method for studying the dynamic behavior of biomolecules, including proteins, DNA, and small molecules. It provides insights into molecular motions, interactions, and the mechanisms underlying biological functions. 1. Introduction to Molecular Dynamics Simulation This document introduces the basic principles of molecular dynamics simulation, including how molecular systems
Molecular Dynamics Simulation Read More »
Introduction to Molecular Dynamics Simulation
Introduction Molecular dynamics (MD) simulation is a computational method for investigating the dynamic behavior of molecules, particularly biomolecules such as proteins, nucleic acids, lipids, and their complexes. In an MD simulation, a molecular system is represented as a collection of atoms whose interactions are described using a predefined mathematical model called a force field. The
Introduction to Molecular Dynamics Simulation Read More »
Activity for Multiple Sequence Alignment
Introduction 본 실습에서는 단백질 서열을 수집하고, Multiple Sequence Alignment (MSA)를 수행하여서열 간의 보존 영역(conserved region)과 가변 영역(variable region)을 분석한다. Multiple sequence alignment 수행 실습 디렉토리 구성 유전자의 단백질 서열 획득 진화적으로 연관된 단백질 서열 정보 획득 Query 서열 추가 Multiple sequence alignment using Clustal Omega Multiple sequence alignment 결과 확인 MSA 결과 확인 보존 영역
Activity for Multiple Sequence Alignment Read More »
Variant calling using GATK
Introduction Germline and somatic variants can reveal the genetic factors underlying a disease or phenotype. These variants are identified by mapping sequencing reads to a reference genome and detecting differences. However, it is necessary to distinguish disease-associated variants from natural genetic variation, such as single nucleotide polymorphisms (SNPs), which are widely distributed across population rather
Variant calling using GATK Read More »
DNA의 3차원 입체 구조
Introduction DNA 분자의 입체 구조는 생명체가 유전 정보를 어떻게 저장하고 전달하는지를 이해하는 데 분자 수준의 통찰을 제공한다. James Watson과 Francis Crick은 DNA의 이중 나선(double helix) 구조 모델을 제시하였으며, 유전 정보가 adenine, thymine, guanine, cytosine의 선형적인 염기 서열 형태로 기록되어 있음을 설명하였다. 또한, 상보적인 염기쌍 형성 원리를 통해 한 가닥의 염기 서열 정보만으로도 반대 가닥이 재구성될
Biomedical Data Analysis: mini-Projects
Introduction mini Project 1: practice to build a simpler database using a complex database (ChEMBL) Drug – target interaction Practice to model a small database (entity – relationship model) using Chembl data mini Project 2: organize your own data for research
Biomedical Data Analysis: mini-Projects Read More »
Example – data visualization
Matplotlib Matplotlib is a general library for plotting data. Scatter plot Bar plot Seaborn Seaborn allows more advanced data visualization, based on matplotlib library. Scatter plot Clustermap
Example – data visualization Read More »
Example – machine learning
Linear Regression Load libraries Load data Divide datasets into training and testing sets Generate a model Machine learning (training): seek for the optimal parameters Make predictions Analyze models Visualize the results
Example – machine learning Read More »