Protein Structures: Determination, Prediction, Modeling, Docking, Simulation, and Visualizations

Protein Structures: represent the three-dimensional arrangement of atoms in amino acids.

Why protein structures are important?

1. To understand the interactions with other proteins or molecules
2. To design inhibitors and drugs
3. To find out B cell epitopes
4. To understand the basic biology

These structures are guided by the protein sequence and therefore linear sequence is also called the primary structure of the proteins.

Ref: https://www.nature.com/scitable/topicpage/protein-structure-14122136/

How structures are determined?

There are many experimental methods to determine the structures, which include:

a. X-ray crystallography: using X-ray diffraction on crystallized proteins.

b. Small Angle X-ray Scattering (SAXS): to determine the shape or boundaries of the proteins.

The other methods are NMR and Cryo-EM.

It's almost impossible or not worth to experimentally determine the structure of every protein or mutant.

How bioinformatics can help in protein structures?

It can offer algorithms and software packages to predict and visualize the structures.

Protein structures could be predicted with great precision.

These methods could be broadly divided into:

• Template-based structure predictions
• Template-free structure predictions

How to proceed once we have the structure in hand?

• Perform docking to design inhibitors
• Perform MD simulation to understand protein behavior or atomic movement under different conditions.

Seeing is believing

Visualize your structures in different environments, with different interactions, and with different binding patterns.

Can we make a research project out of it?

Yes, this is all possible in a single workshop. join us !!!

How to join?

Register at www.dollareducation.org

Dates: 16 May-25 May 2022, 6 PM IST every day

Interactive sessions on Zoom

Affordable fee: INR1200 or USD25

Expert speakers with a combined experience from 100s of publications in high impact journals.

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