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References: Structural Bioinformatics

  1. Protein Structure - Wikipedia - Covers the four levels of protein structure from primary sequence to quaternary assembly, including folding principles, structural motifs, and the relationship between structure and function.

  2. AlphaFold - Wikipedia - Describes DeepMind's AlphaFold system for protein structure prediction, its breakthrough performance at CASP14, the attention-based architecture, and the AlphaFold Protein Structure Database.

  3. Molecular Docking - Wikipedia - Explains computational molecular docking methods for predicting binding poses between proteins and ligands, covering scoring functions, search algorithms, and applications in drug discovery.

  4. Introduction to Protein Structure (2nd Edition) - Carl Branden - Garland Science - Classic textbook on protein architecture covering secondary structure elements, domain folds, protein families, and structure-function relationships with extensive illustrations.

  5. Structural Bioinformatics (2nd Edition) - Jenny Gu - Wiley-Blackwell - Comprehensive reference covering protein structure prediction, comparison, classification, contact maps, molecular visualization, and computational approaches to drug design.

  6. RCSB PDB Documentation - RCSB PDB - Guide to navigating and understanding protein structures in the Protein Data Bank, including search tools, structure validation reports, and 3D visualization features.

  7. AlphaFold Protein Structure Database - EMBL-EBI/DeepMind - FAQ and documentation for accessing over 200 million predicted protein structures, explaining confidence scores, model quality metrics, and programmatic API access.

  8. Mol* Viewer Documentation - Mol Development Team - Documentation for the Mol web-based molecular visualization tool used by PDB, covering 3D rendering, selection language, structural analysis, and session sharing.

  9. SCOP2 Classification - MRC Laboratory of Molecular Biology - Structural Classification of Proteins database organizing protein domains by evolutionary relationships, useful for understanding protein fold space and structural evolution.

  10. Lipinski's Rule of Five - ChEMBL/EMBL-EBI - ChEMBL database for exploring drug-likeness properties, bioactivity data, and molecular descriptors relevant to understanding drug-likeness filtering in structure-based drug design.