1. Protein-Ligand Binding with Applications in Molecular Docking -- 2. Explaining Small Molecule Binding Specificity with Volumetric Representations of Protein Binding Sites -- 3. Machine Learning-based Approaches for Protein Conformational Exploration -- 4. Low Rank Approximation Methods for identifying Impactful Pairwise Protein Mutations -- 5. Detection and analysis of amino acid insertions and deletions -- 6. DeepTracerWeb Service for Fast and Accurate De Novo Protein Complex Structure Prediction from Cryo-EM.

The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved. In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.