LMS Settings
| Module – 6 months | Nucleic Acids MODELING & SIMULATION |
| Topics | – Protein Data Bank (PDB), Nucleic Acid Data Bank (NDB) RCSB, UNIPROT -Introduction to various sequence Databases – Studying Sequence and 2D and 3D structure of DNA/RNA -Learning Visualization tools (Rasmol and Pymol) -Studying Various Motifs in RNA structures – Analyzing H-bonding and Stacking between Nucleobases in RNA – Modeling 3D structure of DNA/RNA – Molecular Dynamics Simulations – Simulation using GROMACS -Analyzing Results – Writing Report |
Nucleic Acids Modeling and Simulations
This course is intended for students and researchers who are intensely interested in learning about the complex architecture of nucleic acid structures. Beginners are welcome to join, even with no previous experience with bioinformatics. However, the candidate must be strongly motivated to learn. Having basic biology and chemistry is a plus for grasping concepts quickly.
Studying Nucleic acid modeling and simulations is essential for understanding the structure and function of DNA and RNA, which are critical biomolecules involved in many crucial biological processes. In addition, nucleic acid modeling and simulations study can provide students with several benefits, including:
Improved understanding of biological processes: By studying nucleic acid modeling and simulations, students can gain a deeper understanding of how DNA and RNA function at the molecular level and how they are involved in various biological processes, such as gene expression and regulation.
Practical skills in computational biology: Nucleic acid modeling and simulations require specialized software and computational techniques, which can help students develop practical skills in computational biology. These skills are in high demand in academia and industry.
Opportunities for interdisciplinary research: Nucleic acid modeling and simulations involve integrating concepts and techniques from multiple disciplines, such as chemistry, biology, and computer science. This multidisciplinary nature can allow students to collaborate on research projects with researchers from different fields.
Career opportunities: The demand for skilled professionals in nucleic acid modeling and simulations is growing as these techniques are increasingly used to study a wide range of biological problems. As such, students who study nucleic acid modeling and simulations may have good job prospects in academia, industry, and government research organizations.
Studying nucleic acid modeling and simulations can give students a deeper understanding of biological processes, practical skills in computational biology, opportunities for interdisciplinary research, and good career prospects.
Who can apply:
- B.Tech. in (Biotechnology/ Industrial Biotechnology/ Bioinformatics/Material Sciences/Computer Sciences)
- M.Sc. in (Biotechnology/Microbiology/Chemistry/Biochemistry/Bioinformatics/Life sciences/Material Sciences)
- M.Tech. in (Biotechnology/Bioinformatics/ Industrial Biotechnology/Computer Sciences)
- B.Pharmacy/ M.Pharmacy
Module (6 Months) Nucleic Acids MODELING & SIMULATION
1
Introduction to various sequence Databases: Protein Data Bank (PDB), Nucleic Acid Data Bank (NDB) RCSB, UNIPROT
An introduction to various sequence databases covers the different types of databases available for storing and accessing biological sequence information. This may include databases for proteins, nucleic acids, and other biomolecules.
The Protein Data Bank (PDB) is a database that stores 3D structural information of proteins and other biomolecules. The Nucleic Acid Data Bank (NDB) is a database that stores 3D structural information of nucleic acids (DNA and RNA). The Research Collaboratory maintains both databases for Structural Bioinformatics (RCSB). UNIPROT is a database that stores information on proteins, including their sequences and functions.
2
Studying Sequence and 2D and 3D structure of DNA/RNA
Studying the sequence and 2D and 3D structure of DNA and RNA involves learning about these biomolecules' chemical and physical properties and how they can be analyzed and visualized using various tools and techniques.
3
Learning Visualization tools (Rasmol and Pymol)
Visualization tools such as Rasmol and Pymol allow users to view and analyze the 3D structure of biomolecules. These tools can be used to study the structure and function of proteins, nucleic acids, and other biomolecules.
4
Studying Various Motifs in RNA structures
Studying various motifs in RNA structures involves identifying and analyzing recurring patterns or structural elements within RNA molecules. These motifs may play a role in the function of the RNA molecule.
5
Modeling 3D structure of DNA/RNA
Modeling the 3D structure of DNA and RNA involves predicting the 3D conformation of these biomolecules based on their sequence and known physical and chemical properties.
6
Molecular Dynamics Simulations
Molecular dynamics simulations allow users to study the movement and behavior of biomolecules over time. In addition, these simulations can provide insights into the function of biomolecules and their interactions with other molecules.
7
Simulation using GROMACS
GROMACS (GROningen MAchine for Chemical Simulations) is a popular software tool for performing molecular dynamics simulations. It is widely used in the fields of chemistry, biochemistry, and biology to study the behavior of biomolecules over time.
In this lecture we will try to cover the following topics:
- Introduction to molecular dynamics simulations: This section could cover the basic principles and concepts of molecular dynamics, including the concept of a force field, the Newtonian equations of motion, and the time integration of these equations.
- Overview of GROMACS: Covering a brief overview of the features and capabilities of GROMACS, including its supported force fields, integrators, and simulation options.
- Setting up a GROMACS simulation: This section will cover the steps involved in setting up GROMACS simulation, including preparing the input files, selecting the appropriate force field and integrator, and setting the simulation parameters.
- Running and analyzing a GROMACS simulation: This section will cover the steps involved in running a GROMACS simulation, including submitting the job to a computing cluster and analyzing the output files. This section will also retouch the previous topic of using visualization tools such as VMD (Visual Molecular Dynamics) to visualize the simulation results.
- Advanced topics: This section will cover more advanced topics such as free energy calculations, umbrella sampling, and replica exchange simulations.
In addition to these topics, this lecture will also include hands-on exercises or demonstrations to give students practical experience with the software.
8
Analyzing Results
Analyzing the results of simulations and experiments involves interpreting and understanding the data generated by these studies. This may involve statistical analysis and visualization of the data.
9
Writing Report
The next Batch starts soon, and Seats are limited. So make sure to register for the course.
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