PRA-MutPred: Predicting the Effect of Point Mutations in Protein-RNA Complexes Using Structural Features.

Interactions between proteins and RNAs are essential for the proper functioning of cells, and mutations in these molecules may lead to diseases. These protein mutations alter the strength of interactions between the protein and RNA, generally described as binding affinity (Δ). Hence, the affinity change upon mutation (ΔΔ) is an important parameter for understanding the effect of mutations in protein-RNA complexes.

Progress on the development of prediction tools for detecting disease causing mutations in proteins.

Proteins are involved in a variety of functions in living organisms. The mutation of amino acid residues in a protein alters its structure, stability, binding, and function, with some mutations leading to diseases. Understanding the influence of mutations on protein structure and function help to gain deep insights on the molecular mechanism of diseases and devising therapeutic strategies.

Protein-nucleic acid complexes: Docking and binding affinity.

Protein-nucleic interactions play essential roles in several biological processes, such as gene regulation, replication, transcription, repair and packaging. The knowledge of three-dimensional structures of protein-nucleic acid complexes and their binding affinities helps to understand these functions. In this review, we focus on two major aspects namely, (i) deciphering the three-dimensional structures of protein-nucleic acid complexes and (ii) predicting their binding affinities.

Tracing ALS Degeneration: Insights from Spinal Cord and Cortex Transcriptomes.

Background/objectives: Amyotrophic Lateral Sclerosis is a progressive neurodegenerative disorder characterized by the loss of upper and lower motor neurons. Key factors contributing to neuronal death include mitochondrial energy damage, oxidative stress, and excitotoxicity. The frontal cortex is crucial for action initiation, planning, and voluntary movements whereas the spinal cord facilitates communication with the brain, walking, and reflexes.

Bioinformatics Approaches for Understanding the Binding Affinity of Protein-Nucleic Acid Complexes.

Protein-nucleic acid interactions are involved in various biological processes such as gene expression, replication, transcription, translation, and packaging. Understanding the recognition mechanism of the protein-nucleic acid complexes has been investigated from different perspectives, including the binding affinities of protein-DNA and protein-RNA complexes. Experimentally, protein-nucleic acid interactions are analyzed using X-ray crystallography, Isothermal Titration Calorimetry (ITC), DNA/RNA pull-down assays, DNA/RNA footprinting, and systematic evolution of ligands by exponential enrichment (SELEX).