Introduction to Cheminformatics

This program is designed for beginners and students who are eager to learn about this fascinating field of computational structural biology and cheminformatics. This collaborative training is prepared and delivered by leaders in various biotechnology and Pharma industries to address the need to introduce students and researchers to utilize public repositories, and open-source tools and to develop quality research projects using structural biology analysis and applying cheminformatics tools. The interested students/researchers will also have the opportunity to learn about the application of R & python for cheminformatics & drug discovery.

It has been well established that discovering and developing drugs is an extensive and expensive process. However, since 2020, there has been a phenomenal demand to increase the use of bioinformatics, cheminformatics, and the use of ML, and artificial intelligence for vaccine and drug development. With the rapidly growing amount of complex healthcare and biological data and the increasing complexities of analysis, every day cutting-edge innovations are bringing new things to learn, hence it is quite challenging for beginners to start their research journey in this fascinating field. To overcome these challenges and bring high-quality summer research training in the field of cheminformatics & drug discovery,  we developed & designed an innovative and industry-driven project-based training opportunity for everyone. 

Topics & Computational Tools (Sessions)

  • Introduction to computational structural biology:  (RCSB Protein Data Bank, PDBSUM, PDBe, PDBj, BMRB, SCOP, and CATH)
  • Introduction to cheminformatics: Structures, Chemical interactions, and Databases  (PubChem, ZINC, ChEMBL)
  • Molecular Visualization, Molecular Modelling, AI for protein folding & prediction (PyMol, UCSF Chimera, Modeller & Alpha Fold)
  • Overview of modern data-driven drug discovery (DataWarrior)
  • Chemical & Protein Databases (Exploration and download data)
  • Structure-based drug discovery (Auto Dock & Argus lab)
  • Advanced Cheminformatics: (Machine learning, Chemical modifications & optimizations )
  • Cheminformatics Research Projects (Industry Projects, Skill Sets, Opportunities & Limitations)

Industry Panel Discussion  Cheminformatics, Bioinformatics & Drug Discovery

The training will be led by the recognized industry leaders and mentors from the elite group of Omics Logic Industry expert panel (FABA, Pine Biotech & Science gurus) to help students, researchers, and scientists utilize structure biology and apply cheminformatics for drug discovery.  This research training is designed to enable students to learn basic concepts of structural biology and to start applying by working and utilizing specialized algorithms and tools that have been utilized by industry and research labs to innovate, discover and answer some of the important biological questions. 


PROGRAM SESSIONS

SESSION TOPICS, MENTORS & RESOURCES

April-2022.006

Mentor: Dr. Mohit Mazumder, Pine Biotech    

Hands-on session: Biomolecular Visualization

Computational Structural Biology

  • Molecular structure of biological macromolecules, History and techniques, Amino acids structure and function, 
  • Protein structures: Primary, Secondary, Tertiary, Quaternary structure, Structural domain, Structural motif, Protein subunit.
  • Protein-Protein Interactions, Conformational analysis, Protein folding, Sequence to structure to function relationship

Tutorial/ Course work:

Basics of structural Biology, History & Biological Repositories and Structure File formats. 

Tools & database: Pymol, Rasmol, RCSB Protein Data Bank, PDBSUM, PDBe, PDBj, BMRB, SCOP, and CATH

April-2022.007

Cheminformatics overview, cheminformatics in drug discovery pipeline, Key-business in cheminformatics

Tutorials:  Chemical Repositories, Small molecule structure File formats 

 Introduction to Cheminformatics
  • Introduction to structure, chemical interaction
  •  Chemical Data: small molecule formulas, structures, properties, spectra, and activities (biological or industrial)
  • Cheminformatics overview, cheminformatics in drug discovery pipeline, Key-business in cheminformatics, 
Hands-on session: Chemical Space exploration 

Course work:

Live session Mentor: Dr.Puneet Kacker, Accenture, India 

Tools & database: Data Warrier, Pubchem & Open-molecules

April-2022.008

Live session Mentor: Dr.Puneet Kacker, Accenture, India 

Hands-on: 

  • Molecular Modelling using Swiss Model and Alpha Fold
  • Tools for 3D structure analysis (Binding Site analysis & predictions)

Target Structure Prediction

  • Overview of Drug Discovery Pipeline, Target prediction & assessment in Industry and Pharma: A case study  
  • Introduction to  3D-Structure prediction: 

Tutorial/ Course work:

Overview of Target structure prediction, Overview of Molecular Modelling: Tutorial: Modeller & Alpha Fold 

Online  Tools & database: Modeller, Swiss-Model, AlphaFold, Chimera, Swiss-Prot & EMBL Repositories  

 

April-2022.009

Mentor: Dr.Puneet Kacker, Accenture, India  

Course work: Chemical & proteins DBs in Drug Discovery process, Tools for data exploration 

Chemical & Protein Databases (Exploration and download data)

  • PubChem: The world's largest collection of freely available chemical information,
  • ZINC: It is a very similar database to Pubchem but with fewer chemicals.
  • ChEMBL: It is a manually curated dataset for bioactive molecules with drug-like properties.
  • RCSB, CAS SciFinder

Hands-on: Data warrior and UCSF chimera.

Tutorial: Exploration and download data:  PubChem, ZINC, ChEMBL, Data warrior 

Tools & database:  PubChem, ZINC, ChEMBL, Drug Bank, Weka, CDK GitHub, Scikit learn, Datawarrior    

April-2022.010

Mentor: Dr.Puneet Kacker, Accenture, India 

Hands-on: Autodock/ArgusLab

  • Practical aspects of ligand conformations, rigidity, and the number of degrees of freedom

Practical experience in Docking 

  • Molecular Docking and stage of Drug Discovery Process 
  • Screening using Public repositories 
  • Ligand target binding, Virtual Screening, target fishing & Profiling, Adverse drug reaction, Pharmacology & Drug repurposing   

Course work: Molecular Docking and stage of Drug Discovery Process 

Tutorials: Autodock & ArgusLab

Tools & database:  Autodock & ArgusLab

Suggested Reading (Links) Provided with the full curriculum

April-2022.011

Mentor: Dr.Puneet Kacker Accenture, India 

Advanced Cheminformatics 

  • Calculation of key Chemical properties
  • Generation of new chemical compounds
  • Identification of chemical representatives

Hands-on Practical sessions on DataWarrior

Tutorial/ Course work:

Advanced Cheminformatics 

Tools & database: DataWarrior

Suggested Reading (Links) Provided with the full curriculum

April-2022.012

Mentor: Dr.Puneet Kacker & Pine Biotech 

Cheminformatics Research Projects: Expert discussions 

  • Designing a cheminformatics research project 
  • Stages of computational research projects
  • Challenges and limitations of computational research projects 
  • Full Drug Discovery Summer program and Omics Logic Research Fellowship

Tutorial/ Course work: Designing a research project & Project Proposal 

Online  Tools & database: Pubmed & Knowledge and Data-Mining logical workflows

April-2022.013

Industry Panel for FABA-Pine Biotech- Other companies Panel Discussion 

Dr. Uday Saxsena, Dr. Ajith Kamath, Prof. Pallu Raddana, Dr. Mohit Mazumder 

Expert Discussions: Cheminformatics, Bioinformatics & Drug Discovery 

Topics for Panel Discussion 

  • Scope of computational cheminformatics in drug discovery 
  • Requirements for the Industry - Skills, Profile, Recognition, and Success 
  • Q&A, Open Stage, Career-related advice for participants
  • Industry networking 

Certification and Research Consultation & Projects 

  • Program and Course Certification

Omics Logic Course and Program Certification, Summary, Progress, and Outcome  
 

 

NOTE : For interested participants in different time zones, the sessions will be recorded and made available to the registered cohort.

Register for the Upcoming Webinar Session & Program details: