last updated 02/2016
Molecular Modelling 
Physical Context 
Description of molecules and their interactions by classical mechanics
Understanding of possibilities and limitations
Advantages and disadvantages of heuristic approaches


Force Fields 
Atom types and energy potentials
Concept of atom types
Bond stretching
Angle bending
Torsions
Electrostatic interactions
Van der Waals interactions

Applications 
Methods using force fields
Geometry optimization
Matrix of second derivatives
Docking
Computer simulations


Examples 
Drugs and their targets
GPCRs
Nuclear receptors
Ion channels
Enzymes
Viral targets

Computer Simulations 
Physical Context 
Description of molecules in solution by statistical thermodynamics
Probabilities
Ergodic hypothesis
Molecular dynamics and Monte Carlo
Fundamental properties


Practical Aspects 
Course of action
Prerequisites
Initial conditions
Boundary conditions
Equilibration
Cutoffs
Electrostatic interactions
Combination of quantum mechanics and classical mechanics

Molecular Dynamics 
Solving the equation of motion
Euler method
Higher order integration methods
Size of the timestep
Constrained dynamics
Timedependend properties
Canonical and NPT ensemble
Restrained dynamics (NMR)
Prediction of free energies


MonteCarlo Integration 
Sampling the configuration space
Separation of phase space
Integrating configuration space
Metropolis algorithm
Movement of rigid bodies

Quantum Chemistry 
Physical Context 
Many electron wave functions
Atomic units
BornOppenheimer approximation
Antisymmetry principle
Atomic orbitals


HatreeFock Approximation 
Single determinant wave functions
Coulomb and exchange operators
Fock operator
Minimization of the energy of a single determinant
Roothaan Equations
Expectation Values and Population Analysis
Polyatomic Basis Sets
Molecular Orbitals

Electron Correlation 
Multi determinant wave functions
Full configuration interaction
Size consistency and size extensivity
Multireference configuration interaction
Coupled Cluster Methods
Manybody pertubation theory


Density Functional Methods 
Approximations by electron density
Local density approximation
Gradient corrections
Hybrid methods
KohnSham equations

Chemoinformatics 
Molecular Representations 
Manipulation and description of molecules
Molecular graphs
Simplified Molecular Input Line Entry Specification
Canonical representation of molecular structures
Substructure searching
3D Pharmacophores
Conformational search
Pharmacophore mapping
2D and 3D descriptors
Fingerprints
Principal component analysis


Molecular Classifications 
Comparison of molecules
Quantitative StructureActivity Relationships
Linear regression
Partial least square
Molecular field analysis
Similarity coefficients
Shape comparison
Scaffold hopping
Cluster analysis
Dissimilaritybased selection methods


Applications 
Searching new lead structures
HighThroughput Screening
Data visualisation
Neural networks
Decision trees
Virtual screening
Oral bioavailability
Docking
ADME/Tox prediction
Design of focused libraries

Bioinformatics 
Sequence Alignment 
Comparison of sequences
Biological databases
Sequence homology
Scoring matrices
Basic Local Alignment Search Tool
Positionspecific scoring matrices
Hidden Markov models
Protein motif and domain prediction
Protein family databases


Applications 
Interpretation of sequences
Gene prediction
Promotor and regulatory element prediction
Construction of phylogenetic trees

Structural Bioinformatics 
Predicting protein and RNA structures
Protein structure hierarchy
Protein structure database
Protein secondary structure prediction
Homology modeling
RNA secondary structure prediction
RNA tertiary structure prediction

Chemistry and the Law 
Exclusive Rights 
Intellectual property rights
Patents
Trademarks
Copyright


Market Access 
Regulatory affairs
REACH
Pharmaceutical regulatory affairs (small molecules, biopharmaceuticals)
