Computational Protein Modeling and Analysis

By Prof. M. K. Verma & Dr. Ashish Patel | Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai

Learners enrolled: 259

This course will focus on the use of efficient technologies used in the protein modeling and its analysis on the basis of the available amino acid or gene sequences.
During this course, candidates learned the introduction to the basic biology required for computational structural designing along with Modeling software. The course includes hands-on exercises on sequence searching (genes & Proteins) and the protein structure design and its analysis approach.

Summary

Course Status :	Completed
Course Type :	Not Applicable
Language for course content :	English
Duration :	12 weeks
Category :	Biological Sciences & Bioengineering
Credit Points :	4
Level :	Diploma
Start Date :	15 Aug 2023
End Date :
Exam Date :

Page Visits

Course layout

Week	Topics	Video Title
Week-1	Cell Biology	Basic Biology-I
	Microbiology	Basic Biology-II
	Virology	Basic Biology-III
Week-2	Molecular Biology	Basic Biology-IV
	Chromosomes and Genes	Basic Biology-V
	Amino acids and Protein Synthesis	Basic Biology-VI
Week-3	History and development of computers, Computer Coding, Number system	Basics of Computer-I
	Languages and flow charts and Operating Systems	Basics of Computer-II
	Modern Computers, Supercomputers, Internet and related programs, Introduction to Biostatistics	Basics of Computer-III
Week-4	Basics about Protein	Introduction to Protein
	Detail about primary structure of Protein	Primary structures of Protein
	Secondary Structure with method of identification	Secondary Structure with method of identification
	Detail about Tertiary Structure	Tertiary Structure
	Detail about Quaternary Structure	Quaternary Structure
Week-5	Introduction to Bioinformatics, Origin and History of Bioinformatics,	Introduction to Bioinformatics
	Introduction to alignment and Types of Alignments Global and. Local alignment	Sequence Alignment
	Pair wise Alignment, Multiple Sequence Alignment	Types of alignment-I
	Clustal W Tool	Types of alignment-II
Week-6	Basic Local Alignment Search Tool with demo	BLAST-I
	Alignment Search Tool with demo	BLAST-II
	Structural determination and Types of Molecular Modeling	Structure Determination and Molecular Modeling
Week-7	Different Types of Search Tools	Database Search
	Details About NCBI	Database Search NCBI-I
	NCBI searching	Database Search NCBI-II
Week-8	Introduction and detail about RCSB	Database Search RCSB-I
Week-8	Searching in RCSB	Database Search RCSB-II
Week-9	Details about Modeler and protein modeling through Modeler	Modeling Software-I
Week-9	Details about different Modeler and protein modeling through other Modeler	Modeling Software-II
Week-10	Introduction and features of SWISS-Model	Modeling Server SWISS-Model
	Introduction and features of The Pipeline	Modeling Server The Pipeline
	Introduction and features of The Workspace	Modeling Server The Workspace
Week-11	Introduction and features of Modeling Server The Repository	Modeling Server The Repository
	Introduction and features of Modeling Server 3D-JIGSAW	Modeling Server 3D-JIGSAW
	Introduction and features of Modeling Server Geno3D	Modeling Server Geno3D
Week-12	Details about Rasmol with Demo	Protein Structure Visualization Tool-I
	Details about Swiss-PDB Viewer with Demo	Protein Structure Visualization Tool-II
	About Procheck tool	Structure Validation-1
	About WHAT IF server	Structure Validation-2
	About PROSA	Structure Validation-3
	Computer, Biology and Modeller	Conclusion and Revision

Books and references

1. Bioinformatics: sequence and genome analysis, 2nd edition Paperback – 1 January 2004

by Mount David W. (Author)

2. Bioinformatics: Sequence and Genome Analysis Paperback – Illustrated, 16 August 2004

3. Introduction to Bioinformatics, T K Atwood, DJ Perry SmithSphukan, Pearson 2009.

5. Introduction to Bioinformatics (Cell and Molecular Biology in Action) Paperback – 8 March 1999 by Dr Teresa Attwood (Author), Dr David Parry-Smith (Author)

6. Introduction to computers, by N. Subramanian, March 2001.

Instructor bio

Prof. M. K. Verma & Dr. Ashish Patel

Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai

Dr. M. K. Verma is currently working as Vice Chancellor in Chhattisgarh Swami Vivekanand Technical University Bhilai (CG). He has vast exposure and experience of 33 years in Research & Academics, Administration and Management. In the field of research and academic, he has published more than 200 research publications in standard journals/conferences have been culminated with a number of recognition and awards. He discharges his duty in NIT Raipur as Dean R & D, Dean Academic Affairs and Dean Student Welfare. He had been Serving Society by providing informal education/training by establishing an independent & self-financed Continuing Education Cell (CEC) and trained more than 2800 persons through 140 one month duration programs. Research guidance and training are also provided in a new upcoming area of Bioinformatics. He has established the Sub-DIC Bioinformatics Center in NIT Raipur funded by DBT, Govt. of India. serving the State and Central Govt. on versatile fronts on various capacity such as Coordinator State Technical Agency (STA) for Chhattisgarh state for NATIONAL RURAL DRINKING WATER PROJECTS (NRDWP), Ministry of Rural Development Government of India, Gazetted member of State Level Expert Appraisal Committee Ministry of Environment & Forest Govt. of India, Coordinator for ‘Chhattisgarh Council of Sc. & Technology’ etc.

Dr Ashish Patel is PhD in Bioinformatics and currently working as Guest Faculty of Bioinformatics and Sr. Consultant in CSVTU Bhilai (CG). He has published more than 150 research papers in the different reputed Journals and International & national conferences. He has completed 3 research projects funded by different state and National Agencies and published 3 books in the domain of Bioinformatics and machine learning. Dr Patel took a copyright for his work of database development in the area of Bioinformatics. He has received many awards in the research and academics. He has received “Young Scientist” award in VIFRA-2015 by center for advance research and design, Tamil Nadu, Venus international Foundation.

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