Protein Folding: From DCA to AlphaFold

This lecture delves into the evolution of protein folding techniques, starting from DCA to the groundbreaking AlphaFold. The instructor explains the concept of pseudo-likelihood and its application in predicting amino acid sequences. The lecture explores the transition from physics-based potentials to co-evolutionary restraints, leading to the development of AlphaFold. It discusses the workflow of direct coupling analysis, the significance of multiple sequence alignment, and the role of deep learning in protein structure prediction. The instructor highlights the improvements brought by AlphaFold, its training process, and the utilization of attention mechanisms and transformers. The lecture concludes by emphasizing the importance of simple methods like DCA in exploring datasets and understanding the evolution of protein folding algorithms.

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Related concepts (19)

PHYS-754: Lecture series on scientific machine learning

This lecture presents ongoing work on how scientific questions can be tackled using machine learning. Machine learning enables extracting knowledge from data computationally and in an automatized way.

Protein folding

Protein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.

Protein structure prediction

Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).

Protein fold class

In molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar amino acid and secondary structure proportions. Each class contains multiple, independent protein superfamilies (i.e. are not necessarily evolutionarily related to one another). Four large classes of protein that are generally agreed upon by the two main structure classification databases (SCOP and CATH).

Evolutionary algorithm

In computational intelligence (CI), an evolutionary algorithm (EA) is a subset of evolutionary computation, a generic population-based metaheuristic optimization algorithm. An EA uses mechanisms inspired by biological evolution, such as reproduction, mutation, recombination, and selection. Candidate solutions to the optimization problem play the role of individuals in a population, and the fitness function determines the quality of the solutions (see also loss function).

Genetic algorithm

In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA). Genetic algorithms are commonly used to generate high-quality solutions to optimization and search problems by relying on biologically inspired operators such as mutation, crossover and selection. Some examples of GA applications include optimizing decision trees for better performance, solving sudoku puzzles, hyperparameter optimization, causal inference, etc.