Protein structure prediction in the context of Simulated annealing


Protein structure prediction in the context of Simulated annealing

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👉 Protein structure prediction in the context of Simulated annealing

Simulated annealing (SA) is a probabilistic technique for approximating the global optimum of a given function. Specifically, it is a metaheuristic to approximate global optimization in a large search space for an optimization problem. For large numbers of local optima, SA can find the global optimum. It is often used when the search space is discrete (for example the traveling salesman problem, the boolean satisfiability problem, protein structure prediction, and job-shop scheduling). For problems where a fixed amount of computing resource is available, finding an approximate global optimum may be more relevant than attempting to find a precise local optimum. In such cases, SA may be preferable to exact algorithms such as gradient descent or branch and bound. The problems solved by SA are currently formulated by an objective function of many variables, subject to several mathematical constraints. In practice, a constraint violation can be penalized as part of the objective function.

Similar techniques have been independently introduced on several occasions, including Pincus (1970), Khachaturyan et al. (1979, 1981), Kirkpatrick, Gelatt and Vecchi (1983), and Cerny (1985). In 1983, this approach was used by Kirkpatrick, Gelatt Jr., and Vecchi for a solution of the traveling salesman problem. They also proposed its current name, simulated annealing.

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Protein structure prediction in the context of AI boom

An AI boom is a period of rapid growth in the field of artificial intelligence (AI). The current boom is an ongoing period that originally started from 2010 to 2016, but saw increased acceleration in the 2020s. Examples of this include generative AI technologies, such as large language models and AI image generators developed by companies like OpenAI, as well as scientific advances, such as protein folding prediction led by Google DeepMind. This period is sometimes referred to as an AI spring, a term used to differentiate it from previous AI winters. As of 2025, ChatGPT has emerged as the 4th most visited website globally, surpassed only by Google, YouTube, and Facebook.

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Protein structure prediction in the context of Demis Hassabis

Sir Demis Hassabis (born 27 July 1976) is a British artificial intelligence (AI) researcher and entrepreneur. He is the chief executive officer and co-founder of Google DeepMind and Isomorphic Labs, and a UK Government AI Adviser. In 2024, Hassabis and John M. Jumper were jointly awarded the Nobel Prize in Chemistry for their AI research contributions for protein structure prediction.

Hassabis is a Fellow of the Royal Society and has won awards for his research efforts, including the Breakthrough Prize, the Canada Gairdner International Award and the Lasker Award. He was appointed a CBE in 2017, and knighted in 2024 for his work on AI. He was also listed among the Time 100 most influential people in the world in 2017 and 2025, and was one of the "Architects of AI" collectively chosen as Time's 2025 Person of the Year.

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Protein structure prediction in the context of John M. Jumper

John Michael Jumper (born 1985) is an American chemist and computer scientist. Jumper and Demis Hassabis were awarded the 2024 Nobel Prize in Chemistry for protein structure prediction.

As of 2025 Jumper serves as director at Google DeepMind. Jumper and his colleagues created AlphaFold, an artificial intelligence (AI) model to predict protein structures from their amino acid sequence with high accuracy. The AlphaFold team had released 214 million protein structures as of January 2024.

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Protein structure prediction in the context of David Baker (biochemist)

David Baker (born October 6, 1962) is an American biochemist and computational biologist who has pioneered methods to design proteins and predict their three-dimensional structures. He is the Henrietta and Aubrey Davis Endowed Professor in Biochemistry, an investigator with the Howard Hughes Medical Institute, and an adjunct professor of genome sciences, bioengineering, chemical engineering, computer science, and physics at the University of Washington. He was awarded the shared 2024 Nobel Prize in Chemistry for his work on computational protein design.

Baker is a member of the United States National Academy of Sciences and the director of the University of Washington's Institute for Protein Design. He has co-founded more than a dozen biotechnology companies and was included in Time magazine's inaugural list of the 100 Most Influential People in health in 2024.

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Protein structure prediction in the context of Structural genomics

Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs.

Because protein structure is closely linked with protein function, the structural genomics has the potential to inform knowledge of protein function. In addition to elucidating protein functions, structural genomics can be used to identify novel protein folds and potential targets for drug discovery. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to a protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure.

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