Algorithms for protein modelling and engineering

By Prof. Pralay Mitra   |   IIT Kharagpur
Learners enrolled: 1699
Proteins are responsible for almost all the functions of the living organism including humans. Understanding proteins interactions and functions helps us to understand disease initiation, progression, and aids in drug design. In this regard Bioinformatics, an interdisciplinary area that deals with designing algorithms for biological problems, is a well-established alternative of cost and resource intensive experimental techniques. In this course we shall discuss the algorithms behind the existing Bioinformatics software tools for protein modeling and engineering so that customization of those software can help us to improve applicability. We shall also discuss some of the unique computational challenges and open areas, solving which can significantly improve human life.

INTENDED AUDIENCE  :  Senior BE/BTech students, Master's students, Ph.D. students, Faculty members, Professionals from Industry. All those who wish to learn and apply their knowledge in either teaching or research on bioinformatics, health care, medical science, pharmacology, drug discovery, etc.

This proposal is derived from the IIT Kharagpur approved PG level course (Computational Biophysics: Algorithms to Applications (CS61060)). While offered in the Spring semester, the course was credited by the UG, PG, and Ph.D. students from various departments including

(i) Computer Science and Engineering,
(ii) Chemical Engineering,
(iii) Electronics & Electrical Communication Engineering,
(iv) Electrical Engineering,
(v) Agricultural and Food Engineering,
(vi) Civil Engineering,
(vii) Biotechnology,
(viii) Physics,
(ix) Chemistry,
(x) Mathematics,
(xi) School of Medical Science and Technology, and
(xii) School of Bioscience.

PREREQUISITES  :  Preliminary knowledge of programming.
INDUSTRY SUPPORT  :  Drug design industries like Novartis, Astrazeneca, Dr. Reddy’s Laboratories, Bharat Biotech International Limited who are working on drug design and pharmacology may recognize this course.
Course Status : Completed
Course Type : Elective
Duration : 12 weeks
Category :
  • Computer Science and Engineering
  • Computational Biology
Credit Points : 3
Level : Postgraduate
Start Date : 26 Jul 2021
End Date : 15 Oct 2021
Enrollment Ends : 09 Aug 2021
Exam Date : 23 Oct 2021 IST

Note: This exam date is subjected to change based on seat availability. You can check final exam date on your hall ticket.

Page Visits

Course layout

Week-1: Introduction
Week-2: Algorithmic techniques for modeling
Week-3: Algorithmic techniques for modeling (Contd.)
Week-4: Algorithmic techniques for modeling (Contd.)
Week-5: Application of REMC and SA on the protein folding problem
Week-6: Protein-protein interaction prediction
Week-7: Protein-protein interaction prediction (Contd.)
Week-8: Protein-protein interaction prediction (Contd.)
Week-9: Algorithm to infer protein assembly in crystals
Week-10: Algorithmic techniques for protein design and engineering
Week-11: Protein design and engineering
Week-12: Role of a score function in protein engineering

Books and references

Text Books

1. Neil C. Jones and Pavel A. Pevzner. An Introduction to Bioinformatics Algorithms. 
2. Bruce R. Donald. Algorithms in Structural Molecular Biology (Computational Molecular Biology). 
3. Burkowski. Structural Bioinformatics: An Algorithmic Approach (Chapman & Hall/CRC Computational Biology Series) 


1. Christopher M. Dobson, Andrej Sali, Martin Karplus. (1998) Protein Folding: A Perspective from Theory and Experiment. Angewandte Chemie International Edition 37(7):868-893. 
2. Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov. (2002) Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins: Structure, Function, and Bioinformatics 47(4):409-443. 
3. Ilan Samish, Christopher M. MacDermaid, Jose Manuel Perez-Aguilar, and Jeffery G. Saven (2011) Theoretical and Computational Protein Design. Annual Review of Physical Chemistry 62:129-149.

Instructor bio

Prof. Pralay Mitra

IIT Kharagpur
Pralay Mitra is an Associate Professor of the Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur. He did his Ph.D. from the Indian Institute of Science Bangalore in 2010 and was a postdoctoral researcher at the University of Michigan, Ann Arbor (from 2011-2013). Dr. Mitra is actively working on Bioinformatics and Computational Biology. Over the years, he developed expertise in modeling and designing protein structures and protein functions. He has developed several algorithms for protein-protein docking, predicting protein assembly from the crystal structures and protein design.

Further details can be found at personal webpage:

Course certificate

The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
Date and Time of Exams: 23 October 2021 Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.


Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Kharagpur .It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team

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