Klaus R. Liedl

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
Electrostatic interactions
Van der Waals interactions


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


Drugs and their targets
Nuclear receptors
Ion channels
Viral targets

Computer Simulations

Physical Context

Description of molecules in solution by statistical thermodynamics
Ergodic hypothesis
Molecular dynamics and Monte Carlo
Fundamental properties

Practical Aspects

Course of action
Initial conditions
Boundary conditions
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 time-step
Constrained dynamics
Time-dependend properties
Canonical and NPT ensemble
Restrained dynamics (NMR)
Prediction of free energies

Monte-Carlo 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
Born-Oppenheimer approximation
Antisymmetry principle
Atomic orbitals

Hatree-Fock 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
Multi-reference configuration interaction
Coupled Cluster Methods
Many-body pertubation theory

Density Functional Methods

Approximations by electron density
Local density approximation
Gradient corrections
Hybrid methods
Kohn-Sham equations


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
Principal component analysis

Molecular Classifications

Comparison of molecules
Quantitative Structure-Activity Relationships
Linear regression
Partial least square
Molecular field analysis
Similarity coefficients
Shape comparison
Scaffold hopping
Cluster analysis
Dissimilarity-based selection methods


Searching new lead structures
High-Throughput Screening
Data visualisation
Neural networks
Decision trees
Virtual screening
Oral bioavailability
ADME/Tox prediction
Design of focused libraries


Sequence Alignment

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


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

Market Access

Regulatory affairs
Pharmaceutical regulatory affairs (small molecules, biopharmaceuticals)
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