Deep Learning for the Life Sciences

Index

Symbols

• 2D3U protein-ligand complex, PDBBind Dataset
  • visualization of, PDBBind Dataset
• 3D protein snapshots (see proteins, structures)

A

• activation functions, Multilayer Perceptrons
  • choices of, Multilayer Perceptrons
• active and decoy molecules, Preparing a Dataset for Predictive Modeling
  • calculated properties of, Preparing a Dataset for Predictive Modeling-Training a Predictive Model
• Adam algorithm, Training Models
• addiction, digital, Learning Models as Therapeutics
• adenine (A), DNA, RNA, and Proteins
• Alzheimer's disease progression, classification with deep learning, X-Ray Scans and CT Scans
• amino acids, Protein Sequences, DNA, RNA, and Proteins
  • common, chemical structures, Protein Sequences
  • residue, PDBBind Dataset
• angstroms, PDBBind Dataset
• antibacterial agents for gram-negative bacteria, Staining
• antibody-antigen interactions, Conclusion
  • modeling antigen-antibody binding, Conclusion
• area under the curve, Training a Model to Predict Toxicity of Molecules
  • (see also ROC AUC scores)
• aromatic rings, Pi-stacking interactions
  • detection with DeepChem RdkitGridFeaturizer, Some implementation details
  • pi-stacking interactions, Pi-stacking interactions
• artifacts of sample preparation, Sample Preparation Artifacts
• AspuruGuzikAutoEncoder class (DeepChem), Working with Generative Models
• atomic featurization, Atomic Featurization
• atomic force microscopy (AFM), Electron and Atomic Force Microscopy
• atoms in molecules
  • chemical bonds connecting, What Is a Molecule?
  • conversion to nodes in molecular graphs, Molecular Graphs ...