Concise parameters and factors to consider when designing a research study and a minute introduction to molecular docking as an approach in computational research studies.

1. INTERACTION PARAMETERS/MOLECULAR DOCKING
UNDERSTANDING BIOMEDICAL
RESEARCH STUDIES:
SOREMEKUN OLADIMEJI

2. CONTENTS
Interactions Parameters
01
Assay Selection
02
Molecular Docking
03

3. INTERACTION PARAMETERS
01

4. Interaction Parameters 🖜
Interaction parameter refers to the
cellular, macromolecular, and atomistic
effects of pathogenic and physiological
interactions in a biological system.
Every research study is designed to assay
for key interaction parameters.

5. Interaction Parameters Assays(I.P.A)
This is the jargon that defines the
experiment type that will carried out
to assess the interaction parameters
in any biological system.
There are two types. They are:
• Biophysical interactions assays
• Biological consequence(s) assays
What is
I.P.A?
Types of
I.P.A
🖜

6. ASSAY SELECTION
02

7. Biophysical Interaction Assays
What are these assays?
Biophysical interactions, which are the macro
and micro- molecular associations in the
living system are assayed through the
following experimental methods.
• Macromolecular Crystallography e.g protein
crystallography
• Computer Aided Drug Design e.g molecular
docking, molecular dynamics simulation.
• Gravimetric Analysis e.g Quartz Crystal
Microbalance(QCM)
• Biolayer Interferometry(BLI).
🖜

8. Biological Consequence Assays
What are these?
We assess the outcome of the biomolecular
interactions taking place in the living
system.
These biological outcomes can be
transcriptomic, proteomic, cellular and/or
morphological.
• Blots e.g western blot, northern blot
• Enzyme-linked Immunosorbent Assay(ELISA)
• Spectrophotometry
• Microscopy
🖜

9. Nota Bene!
How do I choose the right assays
for my study?
🖜
It's vital to remember that identifying and
understanding the relevant biomolecular
pathway(s) will help you choose the best
assay(s) to utilize in your research project.
This only suggests that the selection of an
assay is dependent upon the biomolecular
pathway(s) of the pathogenic condition being
investigated in every given research.

10. MOLECULAR DOCKING
03

11. Molecular docking?
● The goal of ligand-protein
docking/protein-protein
docking is to predict the
predominant binding mode(s)
of a ligand with a protein
of known three-dimensional
structure.

12. Steps involved in molecular docking
Accession and Preparation of implicated
protein targets.
Protei
ns
Accession and Preparation of
compounds/ligands/drugs of study.
Ligand
s
Molecular docking and visualization of the
docking analysis.
D-R
Complex

13. Final
step!
Druglikenes
s
Pharmacokinetic accession of the
ligands of study using various
cheminformatics parameters.
Are they
druggable
?

14. WHY PROTEINS?
The knowledge of your protein
target is the most crucial of all
molecular docking steps.
Protein(s) of study
shouldn’t be retrieved
without prior
understanding of its
structure(tertiary
structure-3D) as this tells
us a lot about it
function(s).

15. UNDERSTANDING
PROTEINS
(To be continued!)

16. Grazie!