MD Simulation Protein-Ligand Complex Online Training

To cater to the need of a huge demand for learning MD Simulations of Protein-Ligand complex we have launched a 5-day Certificate Training Program in MD Simulations | Protein-Ligand complex using Desmond, Maestro for educational purpose in which every day 2-hour interactive training session on Google Meet/Zoom will be conducted to give the user a unique learning experience. Video recording will be provided at the end of the session to give the user a unique learning experience. On successful completion of the course participation certificate will be awarded.

INTRODUCTION
Recently in life science applications, static structure-based approaches, such as docking and virtual screening, have made important strides in advancing drug discovery. MD, especially when coupled with these other computational tools, will open the door to addressing the many drug discovery problems for which the dynamic nature of proteins cannot be ignored, as in the mechanisms of highly mobile membrane proteins and in ligand-induced conformational changes of active sites. In drug designing pipeline protein ligand simulation plays crucial role to understand stability of the system. Another crucial area that can benefit from MD simulation is in the analysis of existing systems, and development of new materials for a wide variety of applications. Many physicochemical phenomena of scientific interest both in life science and materials science occur on time scales that are computationally demanding to simulate. A high-performance MD code, together with continuously advancing computer hardware technologies, can be used to perform simulations on time scales that illuminate these important dynamic processes. Desmond, a newly developed MD code created by DE SHAW RESEARCH, provides parallel scalability, simulation throughput, and scientific accuracy to achieve these goals.
TOPICS
    THEORY AND IMPORTANCE OF PROTEIN- LIGAND SIMULATION
    INTRODUCTION TO DESMOND ENVIRONMENT
    INSTALLATION OF DESMOND
    SETTING UP THE MAESTRO
    CASE STUDY I --SIMULATION OF PROTEIN
    ANALYSIS AND PREPERATION OF MD REPORT
    CASE STUDY II- SIMULATION OF PROTEIN- LIGAND COMPLEX SYSTEM
    ANALYSIS AND PREPARATION OF MD REPORT

PRACTICAL APPLICATION
SCHEDULE
DAY 1: SESSION 1                                                                                                                  2 HOURS
    INTRODUCTION AND IMPORTANCE OF DESMOND
    APPLICATIONS AND ADVANTAGES OF DESMOND
    ABOUT SCHRODINGER DESMOND-MAESTRO
    SETTING UP THE ENVIRONMENT (NVIDIA DRIVERS & CUDA TOOL KIT)
    INSTALLATION OF DESMOND
    LEARNING TO OPEN AND WORK ON MAESTRO PLATFORM BY EXECUTING COMMANDS

DAY 2: SESSION 2                                                                                                                 2 HOURS
EXERCISE CASE STUDY----3LAU (Aurora 2 kinase in complex with GSK3beta inhibitor)
    PROTEIN PREPARATION
    PREPROCESS
    SYSTEM BUILDING
    SOLVATION
    IONIZATION
    MD RUN

DAY 3: SESSION 3                                                                                                                  2 HOURS
1. ANALYSIS FOR DETAILED GENERATION OF REPORTS BY SIMULATION INTERACTION DIAGRAM
     1) RMDS
      2) RMSF
      3) ROG
      4) ENERGY ANALYSIS
      5) TRAJECTORY PLAYING AND ANALYSIS
      6) PROTEIN- LIGAND INTERACTION PLOTS

2. PREPARATION OF PAPER PUBLICATION QUALITY REPORT

DAY 4:  SESSION 4
SIMULATION OF DOCKED COMPLEX                                                                                      2 HOURS
EXERCISE CASE STUDY---6WUU ( SARS COV2 PROTEASE) with curcumin drug docked complex
    PROTEIN PREPARATION
    PREPROCESS
    SYSTEM BUILDING
    SOLVATION
    IONIZATION
    MD RUN

DAY 5: SESSION 5                                                                                                                      1 HOUR
  1. ANALYSIS FOR DETAILED GENERATION OF REPORTS BY SIMULATION INTERACTION DIAGRAM
     1) RMDS
      2) RMSF
      3) ROG
      4) ENERGY ANALYSIS
      5) TRAJECTORY PLAYING AND ANALYSIS
      6) PROTEIN- LIGAND INTERACTION PLOTS

2. PREPARATION OF PAPER PUBLICATION QUALITY REPORT
TARGET AUDIENCE
Student: Bachelor, Masters, PhD, MBBS, MD students as well as Faculty and Professors from Microbiology, Biochemistry, Biotechnology, Immunology, Medicine, Pharmacy, Pharmaceutical Chemistry, Biomedical Technology, Genetics, Bioinformatics, Plant Science and Life Sciences.
Professionals: Resident Doctors, Biotechnology, Bioinformatics, Medicine and Pharmaceutical scientists from industry, academia, and regulatory agencies. Hands-on exercises will be performed individually using software tools on your own laptops. (no prior experience required).
T & C
    Once you register we will send you the schedule of the training.
    It is recommended to provide GMAIL ID for regsitration as the recorded video session will be provided on YouTube.
    Kindly provide that email ID by which you use YouTube.
    Interactive training sessions will be conducted on Google Meet/Zoom 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.
    Video recording of steps will be provided at the end of the session to give the user a unique learning experience.
    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.
    BDG Lifesceiences (OPC) Private Limited is registered under Ministry of MSME(Micro, Small and Medium Enterprises), Government of India with Registration Number:UDYAM-UP-01-0019151 hence the certificate will be provided of it.
    The certificate will be issued as per the details which you will 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.
    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.
    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 (OPC) Pvt. Ltd., India 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.