BIOT F417 BITS Pilani Dubai Campus
BIOT F417 BITS Pilani Dubai Campus
BIOT F417 BITS Pilani Dubai Campus
The course is designed to provide students the first-hand experience of potential utility of biomolecular modeling
especially in concurrent pharmaceutical research, and in cell and structural biology. It describes the functionality,
advantages, and limitations of standard computing strategies for the simulation of biomolecules. Provide a working
knowledge of freely available software to carry out independent research projects in biomolecular modeling and explore
the possibilities for modeling to assist in the process of determination, analyses, evaluation, display, and retrieval of 3D
structure data in a research or industry laboratory environment.
Study Material:
Textbooks:
TB: “Molecular modeling: Principles and Applications” By Andrew R Leach, 2 ndEdition, 2001, Pearson
Education Lim.
Reference books:
RB1: “Molecular Modeling and Simulation - An Interdisciplinary Guide” ByTamar Schlick, Springer, New York,
2002
RB2: “Principles of protein structure” By Schulz, G.E. and Schirmer, R.H., New York, Springer-
Verlag, 1979
RB3: “An Introduction to Computational Biochemistry” – By C. Stan Tsai, Wiley-Liss, Inc, 2002.
RB4: “Bioinformatics: genes, proteins and computers” – Edited by C. Orengo, D. Jones, J. Thornton,BIOS Scientific
Publishers Ltd., UK, 2003.
Lecture Schedule:
# Introduction What is modeling? Scope and application of modeling RB1 (1-2) 1-2
in modern biology
1 Protein structure and Amino acid building blocks, rotameric structures RB1 (3-4) 3-8
conformation protein conformation framework, Ramachandran
plots, conformational hierarchy, structural motifs
2 Conformation and Basic building blocks, conformational flexibility, RB1 (5-6) 9-12
variability in DNA canonical DNA forms, DNA sequence effects
structures
9 Molecular dynamics Basic MD algorithm, its limitation, treatment of long TB (6-7) 33-35
range forces
10 Conformational analysis Analysis of molecular dynamics trajectories TB (9) 36-38
Evaluation Scheme:
* Please refer the link for the PLOs of the B.E. Biotechnology programme.
Mid-sem Grading: Mid-sem grading will be displayed after two evaluation components (Refer Academic calendar for
schedule).
Note: A student will be likely to get “NC”, if he / she doesn’t appear / appear for the sake of appearing for the evaluation
components / scoring zero in the pre-compre total.
Assignments and Projects: Several research-based projects will be assigned from time-to-time to allow the students to
practically apply their knowledge of molecular modelling concepts and tools to solve real-life problems.
Makeup and Attendance policies: Make-ups are not given as a routine. It is solely dependent upon the genuineness of
the circumstances under which a student fails to appear in a scheduled evaluation component. In such circumstances, prior
permission should be obtained from the I/C. The decision of the I/C in the above matter will be final.
Attendance: Every student is expected to be responsible for regularity of his/her attendance in classrooms and
laboratories, to appear in scheduled tests and examinations and fulfill all other tasks assigned to him/her in every course.
A student should have a minimum of 60% of attendance in a course to be eligible to appear for the Comprehensive
Examination in that course. For the students under the purview of Academic Counseling Board (ACB), the Board shall
prescribe the minimum attendance requirement on a case-to-case basis. Attendance in the course will be a deciding factor
in judging the seriousness of a student which may be directly / indirectly related to grading.
General timings for consultation: Students can contact the Course Instructor in her chamber for consultation at mutually
agreeable timings.
General instructions: Students should come prepared for classes and carry the textbook(s) or material(s) as suggested
by the Course Faculty to the class.
Notices: All notices concerning the course will be displayed on the respective Notice Boards.
Instructor-in-Charge
BIOT F417
Contact Details:
Dr. Debostuti Ghoshdastidar, Assistant Professor, Chamber No:316, Contact No: +971 42753700 Ext: 422,
Mob:+971561661433. email: [email protected]
BITSinPILANI,
1. Chamber Consultation Hour: To be announced the class. DUBAI CAMPUS
ACADEMIC - UNDERGRADUATE STUDIES DIVISION
Group. 2. Notices: Notices, if any concerning the course will be displayed on the notice Board of Biology
SECOND SEMESTER 2023-2024
charge 3. Make up Policy: Make up will be given on genuine grounds as determined by the Instructor-in-
DEBOSTUTI GHOSHDASTIDAR
Instructor-in-charge
BIOT F417
1. Course description:
Biomolecular Conformations, Structural genomics and proteomics, protein folding, Forcefield, Simulation,
Conformational analysis, ab initio structure prediction, comparative modeling, lattice models, usage of modeling
packages.