"Hands-on Advanced Molecular Modelling and Simulation"
SARS COVID-19 Case Study
SIMULATE THE FUTURE 29th & 30th January 2021

Workshop Starts in
30

Days

08

Hrs

44

Mins

55

Secs

Program

Introduction to Linux Environment and Bioinformatics
1
Basic Linux Tutorial Dr. Kaushik Chakraborty, CubeBio AI
2
Scripting using Bash/Python Ms. Kajal Pande, Quantumzyme
3
Visualization Tools Dr. Mithun Radhakrishna, IIT Gandhinagar
Molecular Modelling
1
Modelling of SARS-COV2 Protease Prof. Jiri Damborsky, Masaryk University
Molecular Docking and Ligand Parameterization
1
Molecular Docking and Analysis Dr. Shubhandra Tripathi, IIT Kanpur
2
Ligand Parameterization Dr. Abhijit Kayal, Quantumzyme
Molecular Dynamics Simulation
1
Basics of Molecular Dynamics Simulation Prof. Jiri Damborsky, Masaryk University
2
Hands-on Session on MD Simulation Mr. Ashish Malik, Quantumzyme
Inaugural Address

Mr. Narayanan Suresh is the Chief Operating Officer at the Association of Biotech Enabled Enterprises (ABLE), giving him the challenging task to ensure smooth and orderly functioning of the biotech industry, set up a robust information sharing network, interface with policy makers, regulators and the wide range of stakeholders and make organisations the hub of activities for hundreds of start-ups in the biotech sector. He has worked closely with the biotech sector in India as a Science reporter journalist for the Times of India since 1996. Currently, he is instrumental in supporting the start-up ecosystem in Bangalore and is the prime link with the Government.

Mr. Narayanan Suresh
Closing Remarks

Prof. Nair’s work mainly focuses on simulating chemical reactions in condensed matter systems using ab initio or hybrid QM/MM Molecular Dynamics Simulation techniques. Novel QM/MM techniques as well as enhanced sampling techniques are also developed in his group. His group also co-develops the CPMD program package. New atomistic force-fields are also developed to model complex systems like polymer-oxide interface, alumino-silicates, high-performance polymers, and polymer nano-composites.

Professor-Nisanth-Nair
Professor Nisanth Nair

Speakers

Jiri Damborsky
Prof. Jiri Damborsky

Prof. Jiri Damborsky is the Josef Loschmidt Chair Professor of Chemistry at the Faculty of Science at Masaryk University in Brno, Czech Republic and a group leader at the International Centre for Clinical Research. His research focuses on the development of new concepts and software tools for protein engineering. He has published more than 200 original articles, 18 book chapters and filed 7 international patents. He undertook the research visits to The Novo Nordisk Foundation (Denmark); University of Washington, The University of Michigan and University of Tennessee (USA); International Institute of Molecular and Cell Biology (Poland); Umea University (Sweden), University of Groningen and University of Utrecht (The Netherlands) and University of Kent (United Kingdom). He is a co-founder of the first biotechnology spin-off from Masaryk University Enantis Ltd. Among the awards and distinctions, he has received the award EMBO/HHMI Scientist of the European Molecular Biology Organisation and the Howard Hughes Medical Institute.

Dr. Shubhandra Tripathi

Dr. Shubhandra Tripathi has obtained his Ph.D. in life sciences from CSIR-CIMAP, Lucknow. He is currently working as an Institute Postdoc, in the Department of Chemistry at IIT Kanpur with Prof. Nisanth N. Nair. During his Ph.D., he worked on the interaction study of novel compounds with tubulin, a cytoskeleton protein, as a cancer target. His area of expertise includes molecular modelling studies of biomacromolecules using all-atoms Molecular Dynamic Simulations. He is currently working on the enhanced sampling method of Temperature Accelerate Sliced Sampling (TASS) for drug-unbinding studies.

Dr. Mithun Radhakrishna

Dr. Mithun Radhakrishna, is an Assistant Professor in Chemical Engineering at IIT Gandhinagar . His research interests are in the area of protein-surface interactions, protein aggregation & folding and, charge driven self-assembly. He uses the tools of Statistical Mechanics and Molecular Simulations to understand the interactions taking place at the nanoscale. He holds a B.Tech from NIT Tiruchirappalli (2009) and an MS (2010) & Ph.D (2014) from Columbia University, USA. He worked as a Postdoctoral Research Associate at the University of Illinois at Urbana-Champaign before joining IIT Gandhinagar as an Asst. Professor in Dec 2016.

Kaushik Chakraborty
Dr. Kaushik Chakraborty

Dr. Kaushik Chakraborty did Ph.D from Indian Institute of Technology Kharagpur under the guidance of Professor Sanjoy Bandyopadhyay in the field of Computational Chemistry. Then spent 4 years in the City University of New York as a post-doctorate fellow. The focus of research work was to study biological, as well as synthetic macromolecules using Molecular Dynamics Simulation techniques. Currently, Kaushik Chakraborty is working as a Senior Scientist in the CubeBio AI.

Ratul Chowdhury
Dr. Sakshi Piplani

Dr. Sakshi Piplani has obtained her Ph.D. in Bioinformatics from MDU, Rohtak. She is currently working as a Senior Bioinformatics Scientist in Vaxine Pty Ltd, Adelaide. Her area of expertise includes molecular modelling, molecular dynamics simulation. Currently, she is involved in new Artificial Intelligence techniques to identify novel drugs and new scaffolds against specific targets.

Shubhandra Tripathi

Shubhandra Tripathi has obtained his Ph.D. in life sciences from CSIR-CIMAP, Lucknow. He is currently working as an Institute Postdoc, in the Department of Chemistry at IIT Kanpur with Prof. Nisanth N. Nair. During his Ph.D., he worked on the interaction study of novel compounds with tubulin, a cytoskeleton protein, as a cancer target. His area of expertise includes molecular modelling studies of biomacromolecules using all-atoms Molecular Dynamic Simulations. He is currently working on the enhanced sampling method of Temperature Accelerate Sliced Sampling (TASS) for drug-unbinding studies.

Richard

Shubhandra Tripathi has obtained his Ph.D. in life sciences from CSIR-CIMAP, Lucknow. He is currently working as an Institute Postdoc, in the Department of Chemistry at IIT Kanpur with Prof. Nisanth N. Nair. During his Ph.D., he worked on the interaction study of novel compounds with tubulin, a cytoskeleton protein, as a cancer target. His area of expertise includes molecular modelling studies of biomacromolecules using all-atoms Molecular Dynamic Simulations. He is currently working on the enhanced sampling method of Temperature Accelerate Sliced Sampling (TASS) for drug-unbinding studies.

Naveen

Shubhandra Tripathi has obtained his Ph.D. in life sciences from CSIR-CIMAP, Lucknow. He is currently working as an Institute Postdoc, in the Department of Chemistry at IIT Kanpur with Prof. Nisanth N. Nair. During his Ph.D., he worked on the interaction study of novel compounds with tubulin, a cytoskeleton protein, as a cancer target. His area of expertise includes molecular modelling studies of biomacromolecules using all-atoms Molecular Dynamic Simulations. He is currently working on the enhanced sampling method of Temperature Accelerate Sliced Sampling (TASS) for drug-unbinding studies.

Naveen

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Dr.Mithun Radhakrishna

Dr.Mithun Radhakrishna, is an Assistant Professor in Chemical Engineering at IIT Gandhinagar . His research interests are in the area of protein-surface interactions, protein aggregation & folding and, charge driven self-assembly. He uses the tools of Statistical Mechanics and Molecular Simulations to understand the interactions taking place at the nanoscale. He holds a B.Tech from NIT Tiruchirappalli (2009) and an MS (2010) & Ph.D (2014) from Columbia University, USA. He worked as a Postdoctoral Research Associate at the University of Illinois at Urbana-Champaign before joining IIT Gandhinagar as an Asst. Professor in Dec 2016.

richard

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Our Mission

The aim of the workshop is to provide a common platform to explore various computational modelling tools and algorithms that are applied in the area of biology and chemistry. This also paves the pathway for the in silico enzyme engineering which is an emerging trend in the field of biocatalysis.

Session Detail

Day 1

Session 
09.30 am - Opening remarks
10.00 am - Introduction to SARS as a Case Study
10:30 am - Introduction to Homology Modelling
11:00 am - Introduction to Molecular Docking
11:30 am - Break
12:00 pm - Introduction to Molecular Dynamics
1:00 pm - Lunch Break

Day 1

Session 
2:00 pm - Docking: SARS-COVID-19 *
3:00 pm - VMD and Chimera: Visualizing Tools  *
4:00 pm - Break
4:30 pm - Linux command Line: vim editors, tools in Linux *

Day 2

Session 
10:00 am - Apo Simulation in Gromacs *
11:00 am - Ligand Parameterization *
11:30 am - Break
12:30 pm - Talk: Python and Bash Scripting
1:00 pm - Lunch Break

Day 2

Session 
2:00 pm - Complex Simulation: Ligand+Protein *
3:00 pm - Trajectory Analysis *
4:00 pm - Break
4:30 pm - Python and Bash Scripting *
5:30 pm - Closing Remarks
* Hands-on sessions

Session Detail

Day 1 (Session 1)

10.00 am
 
Introduction to SARS as a Case Study
10.30 am
 
Introduction to Homology Modelling
11.00 am
 
Introduction to Molecular Docking
11.30 am
 
Break
12.00 pm
 
Introduction to Molecular Dynamics
1.00 pm
 
Lunch Break

Day 1 (Session 2)

Hands-on: Docking: SARS-COVID-19 - 2:00 pm

Hands-on: VMD and Chimera: Visualizing Tools - 3:00 pm

Break - 4:00 pm

Hands-on: Linux command Line: vim editors, tools in Linux- 4:30

Closing Remarks: 5:30 pm

Day 2 (Session 1)

Hands-on: Apo Simulation in Gromacs- 10 am

Hands-on: Ligand Parameterization - 11:00 am

Break -11:30 am

Talk: Python and Bash Scripting - 12:30 pm

Lunch Break - 1:00 pm

Day 2 (Session 2)

Hands-on: Complex Simulation: Ligand+Protein - 2:00 pm

Hands-on: Trajectory Analysis- 3:00 pm

Break - 4:00 pm

Hands-on: Python & Bash Scripting - 4:30 pm

Closing Remarks: 5:30 pm

Student

3000*

MSME / Startups

8000*

Industry

12500*

*GST applicable

Perks

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#110/8 1st Floor, Lal Bagh Main Road, Krishnappa Layout,
Doddamavalli, Sudhama Nagar,
Bengaluru, Karnataka 560027
workshop@quantumzyme.com

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