INTRODUCTION

BDG LifeSciences is a distinguished bioinformatics company established in 2010 and operates globally. Headquartered in India the company specializes in facilitating workshops, training programs, novel & innovative research projects, and online courses in technologies of bioinformatics & life science. The company is registered under the Ministry of MSME (Micro, Small, and Medium Enterprises), Government of India, with the registration number UDYAM-UP-01-0019151. Recently, BDG Lifesciences, India has authorized BBR Group Pty Ltd., Australia (ACN 608 550 849), to operate its programs in Australia & New Zealand.
With a focus on practical application of technology, where participants work on their own computer/laptop on software/servers,  BDG LifeSciences has been a leader in the sector for the last 14 years. Since its inception, BDG LifeSciences has successfully educated a diverse range of participants globally, including students, scientists, faculty members, professors, and corporate executives

---

Overview

Molecular Dynamics (MD) simulations play a crucial role in understanding biomolecular interactions, with significant applications in drug discovery, protein engineering, and structural biology. To meet the growing demand for learning MD simulations on Linux using GROMACS and on Windows using NAMD, we have launched a 10-day Technical Certificate Online Hands-on Program, Practical Approach in Molecular Modeling Dynamics & Simulations | Insights of Computational Biophysics. This program features daily 90-120 minute interactive training sessions via Google Meet/Zoom, providing participants with a unique learning experience, including video recordings for later review. Participants will gain practical knowledge in modeling biological molecules, solvating proteins, running minimization, equilibration, and simulations, and analyzing results. With a comprehensive overview of protein-ligand interactions using GROMACS, the workshop combines theoretical insights and real-world applications, making it an invaluable opportunity for researchers and professionals seeking to integrate MD simulations into their work. A certificate will be awarded upon successful completion of the course.

OPERATING SYSTEM
WINDOWS 10 WITH I3 OR ABOVE PROCESSOR

---

Learning Objectives

Upon completion of this training, participants will:

1. Understand the principles of molecular dynamics and the importance of protein-ligand interactions.
2. Gain hands-on expertise with GROMACS to simulate protein-ligand complexes.
3. Learn how to set up protein and ligand structures for MD simulations.
4. Understand how to create force fields, run simulations, and analyze findings to determine binding affinity and stability.
5. Be able to simulate protein-ligand binding to determine the most stable conformations.
6. Know how to evaluate important simulation data such as RMSD (Root Mean Square Deviation), RMSF (Root Mean Square Fluctuation), and energy profiling. 

---

Methodology

The program will be conducted in interactive sessions, with a focus on practical training with GROMACS to simulate protein-ligand interactions. This methodology includes:
 

1. Introduction to MD Simulations: An overview of molecular dynamics, force fields, and the significance of simulating protein-ligand interactions.
    
2. Software Setup: Participants will learn how to set up and operate GROMACS on their computer.
    
3. Preparing inputs: Practical training on creating protein structures, ligands, and systems for MD simulations, including tools for protein-ligand docking and setup.
    
4. Simulation Process: Step-by-step instructions for setting up, executing, and troubleshooting MD simulations of protein-ligand complexes with GROMACS.
5. Post-Simulation Analysis: Participants will learn how to analyse simulation findings with software such as VMD (Visual Molecular Dynamics), PyMOL, and other visualisation tools. RMSD, RMSF, and energy estimations are some of the  Key outputs which will be explored..
6. Case Study Application: In a practical case study, participants will be able to apply their knowledge to simulate an actual protein-ligand interaction.

The lessons will include a mix of theory, practical demonstrations, and hands-on experience to ensure a balanced approach to learning.

---

Topics

DAY 1	THEORY INSTALLATION OF NAMD INSTALLATION OF VMD INSTALLATION OF NAMD TUTORIAL FILES
DAY 2	GENERATION OF PDB AND PSF FILES BY PGN SCRIPTING MEANING AND DESCRIPTION OF FILES
DAY 3	SOLVATION IN WATER BOX SOLVATION IN WATER SPHERE
DAY 4	PREPARATION OF CONFIGURATION FILES RUNNING SIMULATION
DAY 5	ANALYSIS OF NAMD-VMD VIRTUAL BOX INSTALLATION SOFTWARE INSTALLATION QTGRACE DISCOVERY STUDIO CHIMERA
DAY 6	GROMACS INSTALLATION RUNNING PROTEIN IN WATER SIMULATION TOPOLOGY PREPARATION SOLVATION
DAY 7	IONIZATION MINIMIZATION EQUILIBRATION [PHASE I] EQUILIBRATION [PHASE II] ANALYSIS
DAY 8	RUNNING PROTEIN-LIGAND COMPLEX SIMULATION PREPARATION OF PROTEIN TOPOLOGY PREPARATION OF LIGAND TOPOLOGY PREPARATION OF COMPLEX FILE PREPARATION OF TOPOLOGY FILE
DAY 9	SOLVATION IONIZATION MINIMIZATION
DAY 10	MAKING INDEX FILES EQUILIBRATION PHASE I EQUILIBRATION PHASE II FINAL MD RUN ANALYSIS AND MOVIE MAKING

---

Why You Should Attend

This event is ideal for:
1. Students and Early Career Researchers: Anyone wanting to obtain practical experience in molecular simulations, particularly those interested in MD simulations or GROMACS, including students (Bachelor’s, Master’s, PhD, MBBS, MD), as well as faculty members and professors from fields such as Microbiology, Biochemistry, Genetics, Plant Science, and Life Sciences.

 2. Drug Discovery Researchers: Experts in drug design and development, with a focus on understanding protein-ligand interaction and stability.

3. Structural biologists and chemists:  Those who research the structural dynamics of proteins and how they interact with tiny molecules.

4. Bioinformaticians and Computational Biologists: People in computational biology who seek to incorporate MD simulations into their research workflows.

---

Practical Takeaways

  After attending this workshop, participants will be able to:

1. Comprehensive skills in MD simulations
- GROMACS-based molecular dynamics simulations can be performed independently.
- Ability to prepare, conduct, and analyze MD simulations for biomolecular systems.
- Confident in troubleshooting frequent errors that arise during MD simulations.

2. Experience with Real-World Applications.
Participants will get practical insights into how MD simulations are used in:
- Structural Biology: Understanding of protein folding, misfolding and conformational changes.
- Biotechnology: Developing biomolecules for industrial and therapeutic uses.
- Genetic research: Involves studying the consequences of genetic changes on molecular structures.

3. Resources & Support

- Students have access to all course resources, including tutorials, guides, and case studies.

- Video records of all sessions are kept for future reference.

- Certificates of participation give significance to your academic or professional profile.

---

Why You Should Attend

1. Learn from Experts: Our instructors have extensive expertise of MD simulations and practical applications in drug development and structural biology.
2. Interactive sessions: GROMACS, the industry's top molecular dynamics software, provides hands-on training and practical demonstrations.
3. Real-world Applications: Focus on simulating protein-ligand interactions using real-life scenarios from drug discovery and structural biology.
4. Hands-on Support: Direct, interactive learning with experts guiding you through each step of the process.
5. Networking opportunities: Engage with professionals and researchers from across the world, growing your network in the field of bioinformatics and computational biology.

---

For More Information

• Upcoming Events: Explore Here
• Video Feedback: Visit our youtube channal

---

Take your research to the next level

Don't miss this opportunity to immerse yourself in the world of Molecular Dynamics Simulations and learn how to simulate protein-ligand interactions with GROMACS. Improve your abilities and stay competitive in the fields of bioinformatics and computational biology!

---

Why Choose BDG LifeSciences for this Training?

BDG LifeSciences is a pioneer in innovative and creative learning programs, consistently introducing courses on cutting-edge topics. This training is meticulously designed to meet industry demands, providing participants with a blend of theoretical insights and practical skills. With expert-led sessions, hands-on exercises, and post-training support, BDG LifeSciences ensures a comprehensive and enriching learning experience tailored to the latest advancements in AI and drug discovery.

---

How To Register

To secure your spot:

• Click on Register Now button and proceed.
• Check the confirmation email which you have got and go through the details.
• For any further queries, feel free to email us at info@bdglifesciences.com

---

Previous Events & Testimonials

Gain insight into our past trainings:

• Video Feedback: Visit our YouTube channel for testimonials.
• Upcoming Training Programs: Explore other upcoming events here.

• Upcoming Online Workshops: Explore other upcoming events here.

---

To get regular updates on Upcoming Job opportunities, Research Projects, Courses, Training and Trainings, kindly join our WhatsApp Channel /  Telegram

---

T & C

• Please provide a GMAIL ID for registration as the recorded video session will be provided on YouTube. Kindly provide that email ID by which you use YouTube.
• Video recording of each session will be provided at the end of the session to give the user a unique learning experience.
• Interactive training sessions will be conducted on Google Meet/Zoom so to give users a better learning experience.
• As it is with a LIVE TRAINER hence practical application, i.e., the experiments/tasks to be performed can be done in the best explainable manner.
• In this Online Workshop, there will be a LIVE trainer who will solve queries along with training.
• The program is SELF-PACED. After each session video of that particular session will be shared with you so you can go through as many times as you want and perfect yourself in the topics & tasks.
• If you miss any session then NO PROBLEM you can still perform the tasks by going through the video of that particular session.
• Make sure you register under the right category. If you register under the wrong category then your registration will be invalid and NO REFUND WILL BE MADE IN THIS CASE. This is your mistake and the company is not responsible for it.
• To avoid this do read the description of the ticket before selecting and proceeding with payment.
• You need to upload your professional ID which can be your Student ID Card or Research Institute ID Card or Company ID Card.
• The certificate will be issued as per the details which you provide in the registration form while registering before payment.
• Once you register relax we will send you the meeting link after the workshop registration gets over.
• We want to make sure that you learn properly hence the training certificate will be given ONLY on successful completion of all the tasks given by the trainer.
• The certificates of all our Online programs are sent by email(softcopy) which has a unique barcode. You can take a print of that on heavy cardstock or photo paper and get it laminated if required.
• The registration is NON-REFUNDABLE and NON-TRANSFERABLE.
• BDG Lifesciences reserves the right of admission in all our programs.
• If you are removed or your registration is canceled then there will be no answer to that. We have our own reasons for such an act of ours
• If we do not wish to give this workshop to any participant then we will refund their amount.
• You should also read the Terms & Conditions page as well as the FAQs page. For any assistance kindly chat with our AI Assistant BioBot on the website www.bdglifesciences.com