DeepMind, an artificial intelligence (AI) subsidiary of Google parent Alphabet, said it has been successful in predicting the shape of nearly every protein in the human body as well as thousands of other proteins found in 20 additional organisms that scientists rely on for their research, including yeast, fruit flies, and mice. This breakthrough is likely to assist researchers to understand human diseases better and find new drugs to treat or cure them. Some scientists have compared the DeepMind project to the international effort to map every human gene. DeepMind said in a blog post it is releasing the database for free. To set up and run the database, it has partnered with the European Molecular Biology Laboratory.

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Earlier this month, two groups unveiled the culmination of years of work by computer scientists, biologists, and physicists: advanced modeling programs that can predict the precise 3D atomic structures of proteins. Last week, the biggest payoff of that work arrived. One team used its newly minted artificial intelligence (AI) programs to solve the structures of 350,000 proteins from humans and 20 model organisms, such as Escherichia coli bacteria, yeast, and fruit flies, all mainstays of biological research. In the coming months, the group says it plans to expand its efforts to all cataloged proteins—some 100 million molecules. “It's pretty overwhelming,” says John Moult, a protein folding expert at the University of Maryland, Shady Grove, who runs a biennial competition called the Critical Assessment of protein Structure Prediction (CASP). Moult says structural biologists have dreamed for decades that accurate computer models would one day augment slow, painstaking experimental methods, such as x-ray crystallography, that map protein shapes with extreme precision. “I never thought the dream would come true,” Moult says. The computer model, called AlphaFold, is the work of researchers at DeepMind, a U.K. AI company owned by Alphabet, the parent company of Google. In fall of 2020, AlphaFold swept the CASP competition, tallying a median accuracy score of 92.4 out of 100 for its predicted structures, well ahead of the next closest competitor ( Science , 4 December 2020, p. [1144][1]). But because DeepMind researchers didn't reveal AlphaFold's underlying computer code, other teams were left frustrated, unable to build on the progress. That began to change this month ( Science , 16 July, p. [262][2]). On 15 July, researchers led by Minkyung Baek and David Baker at the University of Washington, Seattle, reported online in Science that they had created a competing system: a highly accurate protein structure prediction program called RoseTTAFold, which they released publicly. The same day, Nature rushed out details of AlphaFold in a paper by DeepMind researchers led by Demis Hassabis and John Jumper. Both programs use AI to spot folding patterns in vast databases of solved protein structures. The programs compute the most likely structure of unknown proteins by applying those patterns and also considering basic physical and biological rules governing how neighboring amino acids in a protein interact. In their paper, Baek and Baker used RoseTTAFold to create a structure database of hundreds of G-protein coupled receptors, a class of common drug targets. Now, DeepMind researchers report in Nature that they have amassed 350,000 predicted structures—more than twice as many as experimenters have solved in many decades of work. AlphaFold's structures for which the researchers say they have high confidence cover nearly 44% of all human proteins. AlphaFold determined that many of the remaining human proteins were “disordered,” meaning their shape doesn't adopt a single structure. Such disordered proteins may ultimately adopt a structure when they bind to a protein partner, Baker says. They may also naturally adopt multiple conformations, says David Agard, a structural biologist at the University of California, San Francisco. A database of DeepMind's new protein predictions, assembled with collaborators at the European Molecular Biology Laboratory (EMBL), is freely accessible online. “It's fantastic they have made this available,” Baker says. “It will really increase the pace of research.” Because the 3D structure of a protein largely dictates its function, the DeepMind library is apt to help biologists sort out how thousands of unknown proteins do their jobs. “We at EMBL believe this will be transformative to understanding how life works,” says the lab's director general, Edith Heard. “This will be one of the most important data sets since the mapping of the human genome,” adds Ewan Birney, director of EMBL's European Bioinformatics Institute. DeepMind collaborators say that by making it possible to quickly assess how a change in a protein's sequence alters its structure and function, AlphaFold has already spurred the development of novel enzymes for breaking down plastic waste. It has also prompted efforts to better target parasitic diseases. The impacts aren't likely to stop there. The predictions will help experimentalists who solve structures, Baek says. Data from x-ray crystallography and cryo–electron microscopy experiments can be difficult to interpret, Baek and others say, and having a model can help pinpoint the correct structure. “In the short term, it will boost structure determination efforts,” she predicts. “And over time it will also slowly replace [experimental] structural determination efforts.” If that happens, structural biologists won't find themselves out of work. Baker notes that both experimental and computational scientists are already beginning to turn their efforts to the more complex challenge of understanding exactly which proteins interact with one another and what molecular changes happen during these interactions. The new tools will “reset the field,” Baker says. “It's a very exciting time.” [1]: http://www.sciencemag.org/content/370/6521/1144 [2]: http://www.sciencemag.org/content/373/6552/262

Structural biologists are not yet used to the idea that they can just look up anything in a matter of seconds, rather than take years to experimentally determine these things,

The artificial intelligence (A.I.) company DeepMind says it will soon release a database of the shape of every protein known to science -- more than 100 million. That's every structured protein in the human body, as well as in 20 research species, including yeast and E. coli bacteria, fruit flies and mice. Prior to the company's AlphaFold project, which uses artificial intelligence to predict protein shapes, only 17% of the proteins in the human body had their structures identified, according to Technology Review. "It looks astonishingly impressive," Tom Ellis, a synthetic biologist at Imperial College London, told Technology Review. Protein folding is incredibly complex.

AlphaFold 2 paper and code is finally released. This post aims to inspire new generations of Machine Learning (ML) engineers to focus on foundational biological problems.

Dialysis adequacy is an important survival indicator in patients with chronic hemodialysis. However, there are inconveniences and disadvantages to measuring dialysis adequacy by blood samples. This study used machine learning models to predict dialysis adequacy in chronic hemodialysis patients using repeatedly measured data during hemodialysis. This study included 1333 hemodialysis sessions corresponding to the monthly examination dates of 61 patients. Patient demographics and clinical parameters were continuously measured from the hemodialysis machine; 240 measurements were collected from each hemodialysis session. Machine learning models (random forest and extreme gradient boosting [XGBoost]) and deep learning models (convolutional neural network and gated recurrent unit) were compared with multivariable linear regression models. The mean absolute percentage error (MAPE), root mean square error (RMSE), and Spearman’s rank correlation coefficient (Corr) for each model using fivefold cross-validation were calculated as performance measurements. The XGBoost model had the best performance among all methods (MAPE = 2.500; RMSE = 2.906; Corr = 0.873). The deep learning models with convolutional neural network (MAPE = 2.835; RMSE = 3.125; Corr = 0.833) and gated recurrent unit (MAPE = 2.974; RMSE = 3.230; Corr = 0.824) had similar performances. The linear regression models had the lowest performance (MAPE = 3.284; RMSE = 3.586; Corr = 0.770) compared with other models. Machine learning methods can accurately infer hemodialysis adequacy using continuously measured data from hemodialysis machines.

General Adversarial Network (GAN) are a generative modelling approach using deep learning neural networks such as CNN. There are two types of modelling techniques, i) Discriminative modelling and ii) generative modelling. Discriminative models are typical one that are used for classification in machine learning. They take input as features X (image, for image classification) and predict the output Y(probability of the image) for the given features. On the other hand, generative models outputs features X (image) given a random value.

Molecular surfaces are defined by the surface enclosing the 3D structure of a molecule at a certain distance from each atom center. Each point on such a continuous surface is characterized by its chemical (e.g., hydrophobicity, electrostatics) and geometric features (e.g., shape, curvature). From a geometrical perspective, molecular surfaces are considered as 3D meshes, i.e., a set of polygons called faces described in terms of a set of vertices that describe how the mesh coordinates exist in the 3D space [ahmed2018survey]. The vertices can be represented by a 2D grid structure (where four vertices on the mesh define a pixel) or by a 3D graph structure. The grid- and graph-based structures of meshes enable applications of 2D CNNs and GNNs to learn on mesh-based molecular surfaces.

COVID-19 is the disease evoked by a new breed of coronavirus called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recently, COVID-19 has become a pandemic by infecting more than 152 million people in over 216 countries and territories. The exponential increase in the number of infections has rendered traditional diagnosis techniques inefficient. Therefore, many researchers have developed several intelligent techniques, such as deep learning (DL) and machine learning (ML), which can assist the healthcare sector in providing quick and precise COVID-19 diagnosis. Therefore, this paper provides a comprehensive review of the most recent DL and ML techniques for COVID-19 diagnosis.