science

NCU BIOINFO 2021

Takahisa YAMATO @ NU

INTRODUCTION

Hello everyone! Welcome to “BIOINFOMATICS @ Nagoya City University”. In my couple of lectures on Jan 17, and 24, 2022, I will introduce basic theory and application on the “Biomolecular structure and functions studied by molecular simulation techniques”. In particular, I would like to emphasize the impact of Data Science on this field. Nowadays its influence of can be recognized not only on the scientific field but also on many aspects in daily life. As a computaitional biophysisist, I keenly aware how useful it is in finding “important message underlying beneath the simulation/calculation/experimental data” and in visualizing those data in a “really effective way that is easy to be grasped by everyone at a glance”. Since, Data Science is among a quite new techniques, it is often difficult, even for a professional scientists like me, to find either good textbook or educational materials on Data Science. It is, however, a great chance for all of you, espacially for those interested in computer eriented science, to be involved in the development of any sort of Data Scientific Research in its early stage !!! To be a developer or an enduser makes a big difference.

One of a good example outstanding Data Scientific Tools in Molecular Bioscience is “AphaFold” which provides a stat-of-the-art computational tool to predict three-dimensional structure from a given amino acid sequence. For several decades the protein folding problem is one of the most difficult problems in life science. As accumulations of available structural data of biomolecules, however, we will be able to learn something new from a numerous numbers of the entries of the list of correspondence between amino acid sequence and its three dimensional structure.

HIGHLIGHTS

Making it Rain: Cloud-Based Molecular Simulation for Everyone

Making it Rain: Open applications in colab

Reference

AlphaFold Colab

ColabFold - Making protein folding accessible to all

CURP (CURrent calculations for Proteins)

DATABASE

PDB (Protein Data Bank)

PDBj (Protein Data Bank Japan)

MOLECULAR DYNAMICS SIMULATION (MD)

AMBER (Assisted Model Building with Energy Refinement)

NAMD (Nanoscale Molecular Dynamics)

GROMACS

CHARMM(Chemistry at HARvard Macromolecular Mechanics)

SIRAH(Southamerican Initiative for a Rapid and Accurate Hamiltonian)

MOLECULAR GRAPHICS / VISUALIZATION

PyMOL

UCSF Chimera

SIMULATION TOOLS

CHARMM-GUI

CHARMM-GUI nanodisc

CHARMM-GUI nanodisc paper

SIMULATION TRAJECTORY ANALYSIS

Principal Component Analysis I

Principal Component Analysis II

MOLECULAR MODELING

Modeller

MOLECULAR PROPERTY ANALYSIS

CURP (CURrent calculations for Proteins)

RING (Residue Interaction Network Generator)

VLDP web server: Solvent accessibility and volume calculation

Protein Volume

バイオインフォマティクス講義 名古屋市立大学 薬学部 2021 倭 剛久 (名古屋大学)