Prediction of 3D structure from sequence

19 Outubro 2026, 11:00 • António Eduardo do Nascimento Ferreira

The prediction of protein structure (3D) from sequence: a difficult problem in structural biology. The CASP competition. Homology modelling: concept, stages and tools. The quality of the obtained models. Errors and limitations of the results of homology modelling. The portal SwissModel. Template search, modelling and final optimisation by empirical force fields. The Alphafold method. The AlphaFold Protein Structure Database.

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Prediction of structural and functional features from sequence

12 Outubro 2026, 11:00 • António Eduardo do Nascimento Ferreira

General ideas about the classification of proteins. The scope and general mechanism of the prediction of structural and functional features from a protein sequence. Role of MSAs and the inference of signatures. Deterministic patterns, PSSSMs and HMMs. Portals ProSIte and InterPro.

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Resources about protein structure, experimental methods and structural classification

28 Setembro 2026, 11:00 • António Eduardo do Nascimento Ferreira

Resources about protein structure: the Protein Data Bank. Representations, atomic coordinates, sequence annotations. Solving the 3D structure of proteins: atomic coordinates in PDB files. The X-ray crystallography approach. The CATH structural classification.

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General principles about protein structure.

21 Setembro 2026, 11:00 • António Eduardo do Nascimento Ferreira

General principles about protein structure. Composition, structural levels and representations. Subunits. Modern view of the central dogma of molecular biology. Definition of domain. Examples. Difference between domain and subunit.

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