User:Insilico/Books/Computational Medicinal Chemistry

An outline

 * Fundamentals
 * Fundamental interaction
 * Energy
 * Energy level
 * Bioenergetics
 * Biological thermodynamics
 * Intermolecular force
 * Chemical bond
 * Covalent bond
 * Ionic bonding
 * Hydrogen bond
 * London dispersion force
 * Van der Waals force
 * Electric potential energy
 * Dipole
 * Gibbs free energy
 * Thermodynamic free energy
 * Free entropy
 * Enthalpy-entropy compensation
 * Molecular modelling


 * Molecular Mechanics
 * Molecular mechanics
 * Force field
 * Energy minimization
 * Newton's method
 * Gradient descent
 * Conjugate gradient method
 * Ewald summation
 * Molecular dynamics
 * Langevin dynamics
 * Free energy perturbation
 * Thermodynamic integration
 * Simulated annealing
 * Comparison of software for molecular mechanics modeling
 * AMBER
 * GROMACS
 * Monte Carlo method
 * Brownian dynamics


 * Quantum Mechanics
 * Electron configuration
 * Atomic orbital
 * Linear combination of atomic orbitals
 * Molecular orbital
 * Potential energy surface
 * Quantum mechanics
 * Orbital hybridisation
 * Quantum chemistry
 * Ab initio quantum chemistry methods
 * Born–Oppenheimer approximation
 * Electronic correlation
 * Basis set
 * Hartree–Fock method
 * Configuration interaction
 * Multi-configurational self-consistent field
 * Møller–Plesset perturbation theory
 * Density functional theory
 * Semi-empirical quantum chemistry method
 * List of quantum chemistry and solid-state physics software
 * QM/MM
 * ONIOM
 * Quantum Monte Carlo


 * Computational Medicinal Chemistry
 * Drug design
 * Docking
 * Searching the conformational space for docking
 * Scoring functions for docking
 * Macromolecular docking
 * Protein design
 * Protein structure prediction
 * Homology modeling
 * Threading (protein sequence)
 * Structural alignment
 * Structure validation
 * Ramachandran plot
 * Protein subcellular localization prediction
 * Protein pKa calculations
 * BLOSUM
 * List of molecular graphics systems
 * Molecular design software
 * List of protein structure prediction software
 * List of protein secondary structure prediction programs


 * Experimental Methods: Basics
 * X-ray crystallography
 * Nuclear magnetic resonance spectroscopy of proteins
 * Biochemical techniques
 * Molecular cloning
 * Protein methods
 * Northern blot
 * Western blot
 * Southern blot
 * Northwestern blot
 * Electroblotting
 * Protein purification
 * Gel electrophoresis
 * Site-directed mutagenesis
 * Immunostaining
 * Gel electrophoresis of proteins
 * Immunoprecipitation
 * Cryo-electron microscopy
 * Bradford protein assay
 * Affinity electrophoresis
 * Eastern blot
 * Immunocytochemistry
 * Immunoelectrophoresis
 * Immunohistochemistry
 * Isoelectric focusing
 * Dialysis (biochemistry)
 * Dynamic light scattering
 * Immunoassay
 * In vitro recombination
 * Indirect immunoperoxidase assay
 * Instruments used in medical laboratories
 * Scintillation proximity assay
 * Sedimentation equilibrium
 * Size-exclusion chromatography
 * Hydrophilic interaction chromatography


 * Protein Biology and Biochemistry
 * Sequencing
 * Protein sequencing
 * Protein–protein interaction
 * Methods to investigate protein–protein interactions
 * Protein–protein interaction screening
 * Molecular-weight size marker
 * Protein–DNA interaction


 * Basics
 * Standard curve
 * Scatchard equation


 * Cell-based experimental methods
 * MTT assay


 * Ligand-binding
 * Ligand binding assay
 * Enzyme assay
 * Isothermal titration calorimetry
 * Radioligand
 * Surface plasmon resonance