THREE-DIMENSIONAL MODELING

Course objectives

KNOWLEDGE AND UNDERSTANDING The main goal of the course is to provide students with the tools necessary for a detailed and critique analysis of the structure of proteins and their macromolecular complexes using Bioinformatics. The first part of the course is dedicated to the theory of Bioinformatics algorithms. During the second part of the course, students are challenged with practical exercises on the structural analysis of protein models by means of open source software. The course consists of lectures that cover the main topics of the program and practical exercises. Exercises are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules. Beside textbooks, students have access to lectures' slides, scientific articles, and other teaching resources made available trough this web site. APPLYING KNOWLEDGE AND UNDERSTANDING The educational aim of the course is to achieve the necessary knowledge for a critical analysis of the structure of proteins and their interactions. By the end of the course students will have acquired the skills necessary to deal with the analysis and experimental study of biological macromolecules. They will learn how to retrieve protein and nucleic acid coordinates from the PDB database, recognize the fold and use software for a detailed analysis of their structure. MAKING JUDGEMENTS The course is aimed at increasing the ability to critically analyze the sequence and structure of proteins and other biological macromolecules. COMMUNICATION SKILLS The course includes significant activity of classroom discussion aimed at developing the ability of students to transfer skills acquired in support of their arguments. In the final exam, students must solve weblems and eventually take an oral presentation on the structure and function of an assigned protein. LEARNING SKILLS The many advancements of scientific research, particularly in the field of bioinformatics, biochemistry and molecular biology, require a constant updating. For this reason, the course aims to provide the necessary tools to achieve a wider knowledge and to align skills to the advancement in biology and bioinformatics research.

Channel 1
ALESSANDRO PAIARDINI Lecturers' profile

Program - Frequency - Exams

Course program
Introduction to bioinformatics; biological data banks; sequence comparison with dot matrix; and dynamic algorithms; statistical assessment of an alignment; scoring matrices; sequence data bank search; multiple sequence alignment and principles of molecular phylogenesis; profile search; motives; gene prediction; secondary structure and accessibility prediction; structural evolution of proteins. Homology modeling and threading. Structural evolution of proteins; Ab-initio protein structure prediction; molecular mechanics; docking and pharmacoforic prediction; drug design; a programming language: Python.
Prerequisites
Basic knowledge of Chemistry, Mathematics, Physics, Organic Chemistry, acquired in the courses of previous years.
Books
Stefano Pascarella, Alessandro Paiardini - Bioinformatica - Zanichelli, 2010
Teaching mode
The course consists of lessons and lectures that cover the main topics of the program, and practical sessions. Practical sessions are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules.
Frequency
Course attendance is not mandatory, but strongly recommended
Exam mode
Final assessment: Exercises on PC + Oral exam
Bibliography
https://elearning.uniroma1.it/course/view.php?id=4942
Lesson mode
The course consists of lessons and lectures that cover the main topics of the program, and practical sessions. Practical sessions are carried out in a computer room with the use of open source software for the visualization of the tridimensional structure of macromolecules.
  • Academic year2025/2026
  • CourseBiotechnologies
  • CurriculumSingle curriculum
  • Year3rd year
  • Semester1st semester
  • SSDBIO/10
  • CFU6