Dr. Abramyan would like all students to have the following 3 documents available during the second part of class on 1/22.

Dr. Abramyan suggests watching the following videos before lecture on 1/22

A general intro to Schrödinger:

https://www.schrodinger.com/training/videos/drug-discovery

An intro level of what are proteins and drugs and their interactions: 

https://www.schrodinger.com/training/videos/small-molecule-drug-discovery/introduction-drugs-drug-targets-and-molecular

A summary animation on docking: 

https://www.schrodinger.com/training/videos/small-molecule-drug-discovery/protein-ligand-docking

There are many different sites and databases that provide access to information about genes and diseases. The following is a selection of sites you might find helpful. You can search these sites based on several different identifiers for your gene:

• Ensembl Gene ID (e.g. ENSG0000001234)
• Gene Name (e.g. GAPDH)
• Uniprot ID
• PDB ID

Agora

Agora contains information about all the targets on your list and why teams nominated them. It also shows results from gene and protein expression studies of AD patients and non-AD cases.

• Search for your gene using Ensembl ID or Gene Name
• Learn why teams nominated these genes (Nomination Details Tab)
  • How many teams nominated this gene?
  • What kind of analysis did they do?
  • Why was the target selected?
  • What is the predicted therapeutic direction?
• Examine evidence from molecular studies (Evidence Tab)
  • Is RNA significantly higher, lower, or not changed in AD patients?
  • Is protein significantly higher, lower, or not changed in AD patients?
  • NOTE: you can find out if there is a significant association hovering over the red dots on the plot.

Open Targets

The Open Targets site summarizes information from multiple sources and shows a summary of evidence for a gene’s association with different diseases.

• Search for your gene using Ensembl ID or Gene Name
  • NOTE: You can also link to Open Targets from Agora’s Gene Summary Tab
• Examine multiple kinds of evidence for this gene’s association with AD

Protein Data Bank

The Protein Data Bank site hosts protein structures deposited by researchers across the globe.

• Search for your gene using the PDB ID.
• View details about the protein structure for this gene.

UniProt

UniProt contains information about general functions of protein targets.

• Search for your gene using Uniprot ID.
• Learn about this gene’s biological function.

StringDB

StringDB shows protein:protein interactions based on a compilation of many different data sources.

• Search for your gene using Ensembl ID or Gene Name
• Learn interaction partners for this gene.

BrainRNAseq

The BrainRNAseq site provides a summary of RNA expression data from different cell types in the brain for both mouse and human brains.

• Search for your gene using Gene Name
• Learn which cell types this gene is expressed in.

NIAGADS Genomics Database

The NIAGADS Genomics Database site contains information about whether genes have a significant genetic link to AD.

• Search for your gene using Ensembl ID or Gene Name
  • NOTE: You can also link to NIAGADS from Agora’s Gene Summary Tab
• Examine evidence for whether or not this gene is genetically linked to AD.
  • NOTE: if there is a significant association, you will see the message “Genetic Evidence for AD”, in RED below the gene name, as follows:

Here is a list of 20 targets nominated by AD researchers and found on the Agora site. Each team will research 5 targets from the list.

Welcome to the course blog for Designing Drugs: From Chemistry to Cure.

This is intended to be a place to engage with your fellow students about the course. As you write and respond to each other, keep in mind that you will be working together throughout the semester and possibly through the summer.

Please take a moment to introduce yourself in the comments. Here are a few optional questions to help you get started:

• What is your background?
• What is your career plan?
• Why are you taking this course?
• What topics do you think will be the most interesting?