Molecular and Computational Biology

Module Molecular Biology

COMPUTATIONAL BIOLOGY MODULE (4 CFU)

DATABASES AND ANALYSIS: use of genomic and protein databases; derived information: genomic context, with identification of genomic regions and transcripts (NCBI, Ensembl). Evaluation of metabolic pathways. Use of the RefSeq database to determine DNA, RNA, and protein sequences. Databases for phenotypic evaluations and genomic pathologies (OMIM).

ALIGNMENT BETWEEN BIOLOGICAL SEQUENCES: Definitions of match, mismatch, and homology in the comparison between two or more sequences; dynamic programming in sequence alignment (dot-plot matrices and dynamic algorithms). Introduction to gaps as parameters for evaluating an alignment; PAM and BLOSUM substitution matrices; BLAST algorithm in its basic version and variants (MegaBLAST). Statistics related to the alignment performed: e-value and other parameters. Multiple sequence alignment. Construction of a phylogenetic tree. PSSM matrix and Hidden Markov Models

PROTEIN STRUCTURES: Reference to the structure of a protein and experimental methods for detecting 3D structure (NMR, X-ray, Cryo-EM); databases for protein analysis: Uniprot (sequence); PDB and AlphaFold (structure), KEGG and IntACT (protein interactions).

PRINCIPLES OF MOLECULAR DOCKING: application of software for the analysis of contact sites for protein-ligand and protein-protein systems

PRINCIPLES OF MOLECULAR DYNAMICS: basic principles of molecular dynamics and possible applications of the technique, force field generation, minimisation steps, equilibration (NPT and NVT, Berenden barostat, c-rescale, Berendsen thermostat, etc.) and production (time determination and application of external parameters); validation of equilibrated structures and analysis of MD trajectories. 

Variants to classical molecular dynamics: metadynamics and Replica Exchange MD