Lecture 16: Protein Structure Prediction

Protein Secondary Structure Prediction: a Literature Review with Focus on Machine Learning Approaches

DNA sequence, containing all genetic traits is not a functional entity. Instead, it transfers to protein sequences by transcription and translation processes. This protein sequence takes on a 3D structure later, which is a functional unit and can manage biological interactions using the information encoded in DNA. Every life process one can figure is undertaken by proteins with specific functio...

Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction

Secondary structure prediction methods are widely used bioinformatics algorithms providing initial insights about protein structure from sequence information. Significant efforts to improve the prediction accuracy over the past years were made, specially the incorporation of information from multiple sequence alignments. This motivated the search for the factors contributing for this improvemen...

Analysis of Structure Prediction Tools in Mutated MeCP-2

Methyl-CpG-binding protein 2 (MeCP2) belongs to the DNAbinding protein family that selectively binds to DNA methylated CpGislands. MeCP2 acts like a transcriptional repressor, that contains a Nterminal methylated DNA-binding domain (MBD), and a C-terminal transcriptional repression domain (TRD). Mutations in MECP2 gene have been associated to Rett Syndrome a neurological disorder linked to X-ch...

In Silico Prediction and Docking of Tertiary Structure of Multifunctional Protein X of Hepatitis B Virus

Hepatitis B virus (HBV) infection is a universal health problem and may result into acute, fulminant, chronic hepatitis liver cirrhosis, or hepatocellular carcinoma. Sequence for protein X of HBV was retrieved from Uniprot database. ProtParam from ExPAsy server was used to investigate the physicochemical properties of the protein. Homology modeling was carried out using Phyre2 server, and refin...

Lecture 16: Linear Prediction-based Representations