Algorithms for protein modelling and engineering

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.

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