Creating a virtual bioinformatics lab module OER to augment protein structure function capstone courses (Version 1.1 - 2023)

Abstract

A set of 5 bioinformatics interactive H5P lab videos. There are accompanying lesson plans, quizzes, assignment with rubrics, and discussion components with rubrics. The videos focus on showing how to find, identify, manipulate, compare, and understand the sequence and 3D structure of model urease enzyme and an unknown protein. The first two videos illustrate the use of BLAST and PSI-BLAST search against a collection of non‐redundant protein databases, an ExPASy, and on‐line Metabolic Maps search by using the direct links to the GenBank™ entries from the BLAST output at the PDB site. The third video explains multiple sequence alignments/conservation and phylogenetic analysis by aligning the FASTA‐formatted sequences from the ExPASy site. The fourth video describes the use of ChEMBL database to perform a “Target” search of unknown protein sequence, find target associated assays and ligand efficiency data, and explore potential inhibitors/modulators of target protein. The last video is about predicting a protein structure and sequence comparison of proteins based on multiple sequence alignment & existing experimental data using SWISS-MODEL, and UCSF Chimera.