Protein folding problem Flashcards
What is the protein folding problem and why is it important?
The protein folding problem is the question of how the amino acid sequence of a protein dictates its structure. The structure, in turn, determines the protein’s mechanism of action or function. This problem is important because it accounts for nearly a quarter of all Nobel Prizes in Chemistry since 1956 and was named as one of the 125 biggest unsolved problems in science by Science in 2005.
What are the three problems of protein folding?
The three problems of protein folding are the folding code, the computational problem, and the kinetic question. The folding code is the thermodynamic question of how a native structure results from the interatomic forces acting on an amino acid sequence. The computational problem involves predicting the native structure of a protein from its amino acid sequence. The kinetic question pertains to the pathway by which a protein reaches its native structure.
What is Folding@home, and what is its goal?
Folding@home is a distributed computing project designed to perform computationally intensive simulations of protein folding. Its goal is to understand protein folding, misfolding, and related diseases.
How does Foldit work, and what is its unique feature?
Foldit presents unfolded proteins to players in the form of puzzles, allowing them to use their intuition and problem-solving skills to determine the protein’s native structure. Foldit’s unique feature is that it incorporates competition into the game, allowing players to compete for high scores and collaborate to solve protein folding problems.
What is Artificial Intelligence (AI)?
Artificial Intelligence (AI) is a branch of computer science and engineering that aims to create intelligent machines that can perform tasks that typically require human intelligence, such as perception, reasoning, learning, and problem-solving.
What is the Global Distance Test used for in protein structure prediction?
The Global Distance Test (GDT) is used to measure the similarity between the computer-predicted protein structure and the experimentally resolved structure. It ranges from 0 to 100, with higher scores indicating closer matches.
What is CASP in protein structure prediction?
Critical Assessment of Techniques for protein Structure Prediction (CASP) is a bi-annual community-wide blind test to predict unknown protein structures given only the amino acid sequence. It was started in 1994 by John Moult and is used to evaluate the accuracy of computer-based protein structure prediction methods.
What is the significance of DeepMind’s AlphaFold in protein structure prediction?
In 2018, DeepMind’s AlphaFold won CASP 13, and in 2020, AlphaFold 2 won CASP 14. These were major milestones in computer-based protein structure prediction as they demonstrated the effectiveness of deep learning techniques in accurately predicting protein structures.
When was DeepMind founded and when was it acquired by Google?
DeepMind was founded in 2010 and was acquired by Google in 2014.
What is DeepMind’s mission?
DeepMind’s mission is to “solve intelligence to advance science and benefit humanity.”
How do DeepMind’s systems differ from other well-known AIs?
DeepMind’s systems are not pre-programmed, but instead learn from experience using raw pixels as data input, based on a system known as Deep Reinforcement Learning. This is different from other well-known AIs such as IBM’s Deep Blue or Watson.
When did DeepMind become a wholly-owned subsidiary of Alphabet Inc.?
DeepMind became a wholly-owned subsidiary of Alphabet Inc. in 2015.
What is the fundamental protein folding problem?
The fundamental protein folding problem is how do proteins find their native states so quickly. It is also known as Levinthal’s paradox, which refers to the puzzle that a polypeptide chain, due to the very large number of degrees of freedom in an unfolded state, has an astronomical number of possible conformations.
What is Levinthal’s paradox?
Levinthal’s paradox is the observation that if a protein were to sequentially sample all possible conformations, it would require a time longer than the age of the universe to arrive at its native conformation.
What is the folding funnel hypothesis?
The folding funnel hypothesis is the idea that a protein’s native state corresponds to its free energy minimum, and that the energy landscape of protein folding is funnel-shaped.
