Protein Structure Accuracy Prediction with Deep Learning and Its Application to Structure Prediction and Design PDF Download
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Author: Naozumi Hiranuma
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Understanding the rules of protein structure folding has always been one of the central goals in computational biology. Deep learning is gaining popularity in protein machine learning due to its ability to learn complex functions on large amounts of protein geometry data. To help understand the rules of protein folding better, we developed neural networks (DeepAccNet and Pluto) that estimate the error in protein models. In other words, these networks estimate how much a computationally modeled protein structure deviates from its experimentally determined conformation. Approximately two million conformations from 21000 protein sequences located at different local energy minima with a large diversity of errors were sampled and used for training. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution. The network should be broadly helpful in assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. The DeepAccNet methods were selected as top-performing methods for the estimation of model accuracy (EMA) category in CASP14. We extended the accuracy prediction models for proteins to more general chemistry by training graph neural networks on a wide variety of protein and non-protein datasets. We showed that the resulting framework (GAAP) successfully estimates the accuracy of non-protein molecules, such as peptides and Protein-DNA complexes. Our results illustrate how deep learning can impact the efficiency and accuracy of large-scale simulations for both modeling and designing of molecules.
Author: Naozumi Hiranuma
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Understanding the rules of protein structure folding has always been one of the central goals in computational biology. Deep learning is gaining popularity in protein machine learning due to its ability to learn complex functions on large amounts of protein geometry data. To help understand the rules of protein folding better, we developed neural networks (DeepAccNet and Pluto) that estimate the error in protein models. In other words, these networks estimate how much a computationally modeled protein structure deviates from its experimentally determined conformation. Approximately two million conformations from 21000 protein sequences located at different local energy minima with a large diversity of errors were sampled and used for training. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution. The network should be broadly helpful in assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. The DeepAccNet methods were selected as top-performing methods for the estimation of model accuracy (EMA) category in CASP14. We extended the accuracy prediction models for proteins to more general chemistry by training graph neural networks on a wide variety of protein and non-protein datasets. We showed that the resulting framework (GAAP) successfully estimates the accuracy of non-protein molecules, such as peptides and Protein-DNA complexes. Our results illustrate how deep learning can impact the efficiency and accuracy of large-scale simulations for both modeling and designing of molecules.
Author: StoryBuddiesPlay
Publisher: StoryBuddiesPlay
ISBN:
Category : Computers
Languages : en
Pages : 71
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Book Description
AlphaFold 3: Unveiling the Secrets of Life, One Molecule at a Time Demystifying the intricate world of proteins just got a whole lot easier with the arrival of AlphaFold 3. This groundbreaking AI model, developed by DeepMind and Isomorphic Labs, has revolutionized protein structure prediction, a field that has captivated scientists for decades. No longer limited to laborious experimental methods, AlphaFold 3 utilizes the power of deep learning to accurately predict protein structures from their amino acid sequences. This capability unlocks a treasure trove of possibilities for various scientific disciplines. From accelerating drug discovery and personalized medicine to understanding complex diseases and designing novel biomaterials, AlphaFold 3 stands poised to transform our understanding of life at the molecular level. Here's what you'll discover in this comprehensive guide: The Protein Folding Problem Explained: Dive into the challenges of traditionally predicting protein structures and the significance of solving this scientific puzzle. The Rise of Deep Learning: A New Hope for Protein Science: Explore how deep learning has emerged as a powerful tool for tackling complex scientific problems like protein structure prediction. A Deep Dive into AlphaFold: Birth of a Revolutionary AI Model: Learn about the development of AlphaFold by DeepMind, its groundbreaking architecture, and its impact on the scientific community. From AlphaFold 2 to AlphaFold 3: Pushing the Boundaries of Accuracy: Witness the continuous advancements in AlphaFold's capabilities, culminating in AlphaFold 3's ability to predict structures of a wider range of biomolecules beyond proteins. Revolutionizing Drug Discovery: How AlphaFold 3 is Changing the Game: Discover how AlphaFold 3 is accelerating the identification and design of new drugs by providing precise structural insights into protein-drug interactions. Unlocking the Secrets of Diseases: A New Lens for Diagnosis and Treatment: Explore how AlphaFold 3 is transforming our understanding of diseases at the molecular level, paving the way for earlier diagnosis, personalized medicine, and the development of new therapies. Beyond Proteins: Expanding the Horizons of AlphaFold 3: Uncover the exciting potential of AlphaFold 3 in predicting the structures of DNA, RNA, and other biomolecules, leading to a more holistic view of cellular processes. The Future of Protein Science: A Collaborative and Responsible Approach: Delve into the ethical considerations surrounding AlphaFold 3 and the importance of responsible development, open access, and international collaboration to maximize its benefits for humanity. This blog post goes beyond just summarizing the features of AlphaFold 3. It provides a compelling narrative that explores the history, scientific significance, and future potential of this groundbreaking technology. Whether you're a scientist, student, or simply curious about the future of scientific discovery, this guide offers a comprehensive exploration of AlphaFold 3 and its transformative impact on the world of science.
Author: StoryBuddiesPlay
Publisher: StoryBuddiesPlay
ISBN:
Category : Computers
Languages : en
Pages : 58
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Book Description
AlphaFold, a groundbreaking AI system, has cracked the code on protein structure prediction, a challenge that baffled scientists for decades. This book explores the science behind AlphaFold, delving into deep learning, big data, and the inner workings of this remarkable program. Uncover how AlphaFold is revolutionizing protein science, with the potential to accelerate drug discovery, personalize medicine, and design innovative materials. This comprehensive guide explores: The significance of protein structures and the challenges of prediction How AlphaFold leverages deep learning and vast data resources The process of protein structure prediction with AlphaFold, including its strengths and limitations The ethical considerations surrounding AI in protein science The exciting future applications of AlphaFold in various scientific fields Whether you're a scientist, student, or simply curious about the future of biology, this book provides a clear and engaging exploration of AlphaFold and its transformative impact on protein science.
Author: Kristof T. Schütt
Publisher: Springer Nature
ISBN: 3030402452
Category : Science
Languages : en
Pages : 473
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Book Description
Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.
Author: Huzefa Rangwala
Publisher: John Wiley & Sons
ISBN: 111809946X
Category : Science
Languages : en
Pages : 611
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Book Description
A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.
Author: Anna Tramontano
Publisher: John Wiley & Sons
ISBN: 352731167X
Category : Medical
Languages : en
Pages : 226
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Book Description
While most textbooks on bioinformatics focus on genetic algorithms and treat protein structure prediction only superficially, this course book assumes a novel and unique focus. Adopting a didactic approach, the author explains all the current methods in terms of their reliability, limitations and user-friendliness. She provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction, making this a must-have for students and researchers.
Author: Chao Fang (Computer scientist)
Publisher:
ISBN:
Category :
Languages : en
Pages : 132
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Book Description
Protein secondary structure, backbone torsion angle and other secondary structure features can provide useful information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this dissertation, several new deep neural network architectures are proposed for protein secondary structure prediction: deep inception-inside-inception (Deep3I) networks and deep neighbor residual (DeepNRN) networks for secondary structure prediction; deep residual inception networks (DeepRIN) for backbone torsion angle prediction; deep dense inception networks (DeepDIN) for beta turn prediction; deep inception capsule networks (DeepICN) for gamma turn prediction. Every tool was then implemented as a standalone tool integrated into MUFold package and freely available to research community. A webserver called MUFold-SS-Angle is also developed for protein property prediction. The input feature to those deep neural networks is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, HHBlits profile and/or predicted shape string. The deep architecture enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, the proposed deep neural architectures outperformed the best existing methods and other deep neural networks significantly: The proposed DeepNRN achieved highest Q8 75.33, 72.9, 70.8 on CASP 10, 11, 12 higher than previous state-of-the-art DeepCNF-SS with 71.8, 72.3, and 69.76. The proposed MUFold-SS (Deep3I) achieved highest Q8 76.47, 74.51, 72.1 on CASP 10, 11, 12. Compared to the recently released state-of-the-art tool, SPIDER3, DeepRIN reduced the Psi angle prediction error by more than 5 degrees and the Phi angle prediction error by more than 2 degrees on average. DeepDIN outperformed significantly BetaTPred3 in both two-class and nine-class beta turn prediction on benchmark BT426 and BT6376. DeepICN is the first application of using capsule network to biological sequence analysis and outperformed all previous gamma-turn predictors on benchmark GT320.
Author: Ilan Samish
Publisher: Humana
ISBN: 9781493966356
Category : Science
Languages : en
Pages : 0
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Book Description
The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Author: Maxim V Shapovalov
Publisher:
ISBN:
Category :
Languages : en
Pages : 164
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Book Description
Proteins are large biomolecules which are functional building blocks of living organisms. There are about 22,000 protein-coding genes in the human genome. Each gene encodes a unique protein sequence of a typical 100-1000 length which is built using a 20-letter alphabet of amino acids. Each protein folds up into a unique 3D shape that enables it to perform its function. Each protein structure consists of some number of helical segments, extended segments called sheets, and loops that connect these elements. In the last two decades, machine learning methods coupled with exponentially expanding biological knowledge databases and computational power are enabling significant progress in the field of computational biology. In this dissertation, I carry out machine learning research for three major interconnected problems to advance protein structural biology as a field. A separate chapter in this dissertation is devoted to each problem. After the three chapters I conclude this doctoral research with a summary and direction of our future work. Chapter 1 describes design, training and application of a convolutional neural network (SecNet) to achieve 84% accuracy for the 60-year-old problem of predicting protein secondary structure given a protein sequence. Our accuracy is 2-3% better than any previous result, which had only risen 5% in last 20 years. We identified the key factors for successful prediction in a detailed ablation study. A paper submitted for publication includes our secondary-structure prediction software, data set generation, and training and testing protocols [1]. Chapter 2 characterizes the design and development of a protocol for clustering of beta turns, i.e. short structural motifs responsible for U-turns in protein loops. We identified 18 turn types, 11 of which are newly described [2]. We also developed a turn library and cross-platform software for turn assignment in new structures. In Chapter 3 I build upon the results from these two problems and predict geometries in loops of unknown structure with custom Residual Neural Networks (ResNet). I demonstrate solid results on (a) locating turns and predicting 18 types and (b) prediction of backbone torsion angles in loops. Given the recent progress in machine learning, these two results provide a strong foundation for successful loop modeling and encourage us to develop a new loop structure prediction program, a critical step in protein structure prediction and modeling.
Author: Yaoqi Zhou
Publisher: Humana
ISBN: 9781493964048
Category : Science
Languages : en
Pages : 0
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Book Description
This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.
