GPCRs
How many transmembrane helices do GPCRs have?
7 ya dumbo
What multi-national investment group had a research branch that developed the first customized hardware for molecular dynamics simulations?
D.E. Shaw Group
What is the name of a popular Python library for training and evaluating many different traditional machine learning and statistical learning methods?
Scikit-Learn
What percentage of FDA approved drugs target GPCRs?
How long does Glide SP take to dock 1 molecule to 1 protein? Round to order of magnitude for first pick.
10 s
Which major cellular signaling pathways (e.g. second messenger systems) do GPCRs modulate?
What is the standard time step used for all MD simulations in our lab?
4 fs, based on hydrogen mass repartitioning
What commonly used machine learning optimization algorithm uses weighted moving averages of gradients and squared gradients in addition to standard gradient descent?
How many novel drugs did the FDA approve in 2024?
50 new drugs, 31 approvals were small molecules
What steps must be taken to prepare a series of ligands in SMILES format for docking?
Tautomerization
Ionization
Stereoisomer Enumeration
3D Conformer Generation
What was the first GPCR to have its crystal structure solved AND when was it solved?
Bovine Rhodopsin in 2000
In MD simulations, what algorithm from statistical mechanics for obtaining a sequence of random samples from a probability distribution where direct sampling is hard is used?
Metropolis algorithm OR
Metropolis-Hastings OR
Markov Chain Monte Carlo
ARES, an RNA structure prediction method released by the Dror Lab, uses what architecture to maintain rotational and translational equivariance?
E3NN OR
Tensor Field Networks
What percentage of drugs from the top 20 pharmaceutical companies that enter Phase 1 trials ultimately get FDA approved?
~10%
What was the first published molecular docking method?
DOCK, 1982
Which family of GPCRs is associated with Dishevelled proteins, and was originally discovered from flies with bad hair?
Class Frizzled GPCRs
What decade was molecular dynamics first applied to simulate proteins?
1970s (1977), McCammon, Gelin, Karplus
AlphaFold uses a 2 transformer tower architecture that operates on what 2 types of representations? What is the architecture called?
MSA Representation AND
Pair Representation
How much did Keytruda, the highest grossing drug of 2024, make in annual sales? Must be within 10% of the true cost for first picks.
$30 Billion Dollars
Given a rigid protein pocket, what is a major energetic term that is poorly accounted for in docking scoring functions?
Ligand Strain & Ligand Entropic Penalty OR
Energy of Solvation for the Ligand and Protein
What decade was the existence of GPCRs as individual purified proteins first confirmed?
1980s by Bob Lefkowitz and Marc Caron working on B2, A2A and A1B
How much does Amber24, a popular MD engine and force field, cost for commercial users? Must be within 10% of the true cost for first picks.
$25,000 per site Amber24 is used
Ron completed his qualifying examination work on applying what types of machine learning approaches to gene array data denoising / transcript estimation?
Bayesian Modeling / Bayesian Neural Networks
What year did clinical trials first start for semaglutide (now marketed as Ozempic) in the U.S.?
2008, Phase 2 trials
What is the claimed Diff-Dock L pose-prediction accuracy at a <2 A threshold for re-docking on unseen sets?
23%