Modeling and Simulation

Recommended Prerequisites

BSc in Medicinal Chemistry, Chemistry, Biochemistry, Bioanalytical Sciences Medical Sciences.

Teaching Methods

This course is based on theoretical and theoretical -practical. The first will be made to give the basis for the underlying matter, fostering dialogue in class and autonomous research students after. The practical classes will be devoted to capacity building in the use of relevant software. For example, we SPSS for statistics, Tinker or Gromacs to force field methods, Gamess for ab initio calculation, VMD for viewing, etc. The student should be able to prepare an input, to calculate and interpret the results.

Learning Outcomes

Provide knowledge in a broad set of numerical techniques, ranging from basic statistics, sampling and modeling to the more usual simulation techniques and calculation of molecular properties. Allow the development of relevant case studies. Make the student capable of using recent techniques in chemoinformatics. The student is made capable of carrying out basic projects, with the ability for a smooth transition towards more complex tasks.

Work Placement(s)

No

Syllabus

• Basic Statistics • Modelling Least squares fitting (linear and nonlinear). Homoscedasticity. Uncertainty. Residuals. Partial least squares. • Sampling Building the sample: type of collection, sample type, size. • Simulation with classical mechanics Statistical mechanics. Force field and force field methods: molecular mechanics, molecular dynamics and Monte-Carlo. • Electronic structure calculations and molecular properties. Ab initio methods, semiempirical and DFT. Calculation of molecular properties. • Molecular modeling of proteins Databases in protein structure analysis. Programs for visualization and analysis of protein structure. Protein structure via homology. • Interaction-binding protein molecular docking • Structure-function relationships in proteins QSAR, quantitative structure-function relationships. Identification and construction of pharmacophore models. • Virtual screening of drugs Research methods 2D and 3D.

Head Lecturer(s)

Jorge Manuel Campos Marques

Assessment Methods

Assessment
Project: 40.0%
Exam: 60.0%

Bibliography

R. Leach, Molecular Modeling. Principles and Applications, 2nd ed., Pearson (2001);

D. C. Rapaport, The art of molecular dynamics simulation, 2nd ed., Cambridge (2004);

I. Levine, Quantum Chemistry, Prentice (2009).