BITS PILANI, DUBAI CAMPUS

ACADEMIC - UNDERGRADUATE STUDIES DIVISION

SECOND SEMESTER 2023-2024
Course Handout (Part II)

BITS PILANI, DUBAI CAMPUS

ACADEMIC - UNDERGRADUATE STUDIES DIVISION Date: 05/02/2024
SECOND
In addition to part -I (General Handout for all SEMESTER
courses appended 2023-2024
to the time table) this portion givesfurther specific
details regarding the course.

Course No. : BIOT F417

Course Title : Biomolecular Modeling
Course Instructor : Debostuti Ghoshdastidar
Instructor in Charge : Debostuti Ghoshdastidar

Scope and objective of the course:

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.

Course Pre/Co-requisite (if any) & Catalogue / Bulletin Description

As given in the Bulletin 2023 – 2024

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

Please Do Not Print Unless Necessary

 BITS PILANI, DUBAI CAMPUS
ACADEMIC - UNDERGRADUATE STUDIES DIVISION
SECOND SEMESTER 2023-2024
Course Handout (Part II)
3 Molecular graphics Introduction to graphic representation, representation of RB3 (4) 13-14
molecularBITS PILANI,
structure: DUBAI
both small CAMPUS
molecules and
Macromolecules database of
ACADEMIC - UNDERGRADUATE STUDIES macromolecular structuresDIVISION
4 Visualization and Usages ofSECOND SEMESTER
freely available 2023-2024
visualization packages like Class- 15-17
modeling packages VMD, RASMOL, PYMOL, SPDBVIEWER , Notes/we
CHIMERA, CN3D bsites
5 Protein structure First principle methods for predicting protein structure, RB4(8-9) 18-22
prediction and comparative modeling, threading , CASP, protein
protein folding problem folding theories
6 Energetics and forcefield Different types of interactions and formulation of TB (4) 23-25
forcefield
7 Molecular mechanics Basic algorithm of MM and their utilities, hand on TB (5) 26-30
sessions
8 Monte Carlo simulation Basics of Monte Carlo sampling TB (8) 31-32

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

11 Lab on MD Hand on session on molecular dynamics Amber 39-42

Package

Course Learning Outcomes (CLOs)

Upon successful completion of this course, students should be able to:

• CLO1 Illustrate the structure and conformation of biomolecules based on fundamental rules of chemical
bonding, conformation, configuration and symmetry.
• CLO2 Identify the correlation between the biomolecular structure related question that needs to be answered
and the modeling tool that needs to be employed.
• CLO3 Investigate biomolecular structure and interactions using state-of-the-art visualization tools.
• CLO4 Formulate force field parameters for novel molecules.
• CLO5 Apply the fundamental principles of molecular mechanics in modelling biomolecules, inter-molecular
interactions, and drug design.
• CLO6 Simulate relevant biomolecular complexes, analyze trajectories and deduce results.

Evaluation Scheme:

EC Evaluation Components Nature of Duration Weightage Date & Time Venue

No Component
1 Quiz I Open/Closed book 25 mins 5% 14.03.2024 (Th9) 210
2 Mid Sem Exam Closed book 90 mins 25% 01.04.2024 (FN) TBA
3 Quiz II Open/Closed book 15 mins 10% 16.05.2024 (Th9) 210
4 Assignments/ Projects - - 20% Several

5 Comprehensive Open/Closed book 3 hours 40% 30.05.2024 (FN) TBA

Examination

Please Do Not Print Unless Necessary

 BITS PILANI, DUBAI CAMPUS
ACADEMIC - UNDERGRADUATE STUDIES DIVISION
SECOND SEMESTER 2023-2024
Course Handout (Part II)
Mapping of CLOs, PLOs, and CECs
BITS PILANI, DUBAI CAMPUS
Evaluation Components (ECs)
CLOs PLOs ACADEMIC
EC1
- UNDERGRADUATE
EC2
STUDIES EC4
EC3
DIVISION EC5
CLO1 1, 2 ✓
SECOND SEMESTER
✓
2023-2024 ✓
✓ ✓
CLO2 3, 7 ✓ ✓ ✓ ✓ ✓
CLO3 8 ✓ ✓
CLO4 4, 5, 7 ✓ ✓
CLO5 3, 4, 5, 7 ✓ ✓ ✓
CLO6 3, 4, 5, 7 ✓ ✓

* 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]

Please Do Not Print Unless Necessary

 BITS PILANI, DUBAI CAMPUS
ACADEMIC - UNDERGRADUATE STUDIES DIVISION
SECOND SEMESTER 2023-2024
Course Handout (Part II)

BITS PILANI, DUBAI CAMPUS

ACADEMIC - UNDERGRADUATE STUDIES DIVISION
SECOND SEMESTER 2023-2024

Please Do Not Print Unless Necessary

 BITS PILANI, DUBAI CAMPUS
ACADEMIC - UNDERGRADUATE STUDIES DIVISION
SECOND SEMESTER 2023-2024
Course Handout (Part II)

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.

Please Do Not Print Unless Necessary