User:Insilico/Books/Computational Medicinal Chemistry
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Computational Medicinal Chemistry[edit]
An outline[edit]
- 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