THREE-DIMENSIONAL MODELING

Course objectives

The teaching consists of two modules: "Structural Biology" and "Structural Bioinformatics", each with 3 CFU, for a total of 6 CFU. The training objectives were defined to provide students with a thorough and integrated knowledge of biological structures and bioinformatics tools used to analyse them, with particular emphasis on pharmaceutical applications. General objectives of the course: Interdisciplinary Competence: Contribute to the training of professionals who are able to integrate knowledge of biology and structural bioinformatics and apply this integrated knowledge in research and development of new drugs. Analytical and Critical Skills: Develop the ability to critically analyze molecular structures and biological interactions through experimental and computational approaches. This course aims, within the context of the entire Pharmaceutical Biotechnology course, to provide the specific knowledge needed to prepare students for the scientific and technological challenges in the field of pharmaceutical biotechnology, providing them with the tools they need to contribute effectively to research and development of new therapies. Specific objectives: Module 2: Structural Bioinformatics (3 ECTS) Preliminary: understanding the biological and evolutionary context as a prerequisite for bioinformatic analyses 1. Bioinformatics tools and techniques for structural analysis: • Knowledge and use of the main bioinformatics databases • Understand and apply the main tools for sequence alignment and database search and be able to critically interpret results • Understand and apply the main tools of prediction and analysis of sequence-based three-dimensional structures including hints to machine learning and its applications in bioinformatics • Know how to use the basic functions of integrated sequence and structure analysis tools 2. Molecular Modelling and Simulations: • Know how to use the basic functions of the main tools for molecular graphics and structural analysis: ChimeraX or PyMOL • Learn the theoretical basis of molecular modelling, including structural prediction through homology and de novo and use of related resources. • Understand the basic concepts of molecular dynamics 3. Computational analysis and data interpretation: • Develop skills in structural data analysis using computational methods. • Understand the limits of techniques and fields of application • Interpret the results of bioinformatic analyses and integrate this information to apply it to biotechnology and pharmaceutical problems.

Channel 1
STEFANO PASCARELLA Lecturers' profile

Program - Frequency - Exams

Course program
Description of the main biological databases and interrogation methods (2 hours) - Comparison of two sequences with exact and heuristic algorithms; comparison of two genomes (2 hours) - Score matrices (1 hour) - Searches in databases for sequence similarity (3 hours) - Methods for calculating multiple sequence alignments (4 hours) - Construction of profiles and PSSM (2 hours) - Searches with profiles in databases; profile databases (2 hours) - Hidden Markov Models (HMM) and use for database searches, sequence alignment, protein structure prediction, gene prediction (2 hours) - Neural networks and automatic classification algorithms; application to the prediction of secondary structures, solvent accessibility, signal peptides, antigenic epitopes, protein-protein interaction zones (2 hours) - Use of molecular graphics programs (2 hours) - Modeling by homology (2 hours)
Prerequisites
The optional course takes place in the second semester of the third year. To follow successfully, the student must possess: - notions of biological chemistry (protein structure, enzyme concept, basics of metabolism) - notions of Molecular Biology (concept of gene, genome, structure of nucleic acids, regulation of gene expression) - basic notions of statistics and probability theory (probability, probability distribution, statistical tests) - basic knowledge of the use of computers and internet browsing.
Books
The teaching material is available on the elearning site in the form of video lessons and pdf files. During the course, servers available on the internet and free programs will be used. Optional text: Pascarella Paiardini, Bioinformatics, Zanichelli
Teaching mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
Frequency
Attendance is optional but strongly recommended
Exam mode
The exam aims to verify the level of skill acquired in selecting and using the tools illustrated during the course. The evaluation is expressed out of thirty (minimum grade 18/30, maximum grade 30/30 with honors). The exam is divided into a practical test and a short interview. The practical test consists in solving three problems through the use of bioinformatics programs while the interview focuses on the discussion of the paper and on general theoretical topics. The final vote takes into account the two tests.
Bibliography
Loman, N., Watson, M. So you want to be a computational biologist?. Nat Biotechnol 31, 996–998 (2013). https://doi.org/10.1038/nbt.2740
Lesson mode
Attendance of teaching lessons is not mandatory. The course is structured in theoretical and practical lessons that are held in a computerized classroom. The classroom is covered by the Sapienza WiFi signal and therefore students can also use their laptop for the practical part of the lessons. The theoretical part is illustrated through PowerPoint presentations and video projection of surfing websites. The practical part is carried out at the same time as the theoretical part using the sites that provide the bioinformatics methods described on your computer or on the computers available in the classroom. The practical part is interactive and allows the discussion and analysis of the results of the practical exercise carried out together with the teacher. The elearning2.uniroma1.it site contains the material shown during the lesson and the practical exercises that can thus be repeated autonomously and independently by the student, even remotely. The actual procedures will be decided on the basis of the current anticovid regulations.
  • Academic year2025/2026
  • CoursePharmaceutical Biotechnology
  • CurriculumSingle curriculum
  • Year1st year
  • Semester2nd semester
  • SSDBIO/10
  • CFU3