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Deep Learning To Predict Protein Backbone Structure From High Resolution Cryo Em Density Maps
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Book Synopsis Deep Learning to Predict Protein Backbone Structure from High-resolution Cryo-EM Density Maps by : Spencer Moritz
Download or read book Deep Learning to Predict Protein Backbone Structure from High-resolution Cryo-EM Density Maps written by Spencer Moritz and published by . This book was released on 2019 with total page 42 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Deep Learning for Validating Resolution and Detecting Secondary Structure Elements of Proteins in 3D Cryo-electron Microscopy Images by : Todor Kirilov Avramov
Download or read book Deep Learning for Validating Resolution and Detecting Secondary Structure Elements of Proteins in 3D Cryo-electron Microscopy Images written by Todor Kirilov Avramov and published by . This book was released on 2019 with total page 130 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Deciphering Protein Complex Structures from Cryo-electron Microscopy Maps Using Deep Learning by : Jonas Pfab
Download or read book Deciphering Protein Complex Structures from Cryo-electron Microscopy Maps Using Deep Learning written by Jonas Pfab and published by . This book was released on 2020 with total page 58 pages. Available in PDF, EPUB and Kindle. Book excerpt: Information about macromolecular structure of protein complexes such as SARS-CoV-2, and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for fast de novo multi-chain protein complex structure determination from high-resolution cryo-electron microscopy (cryo-EM) density maps. We applied DeepTracer on a previously published set of 476 raw experimental density maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer and the RMSD value improved from 1.29Å to 1.18Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related density maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average RMSD of 0.93Å. Additional tests with related methods further exemplify DeepTracer's competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only two hours. The web service is globally accessible at https://deeptracer.uw.edu.
Book Synopsis Biochemical and Molecular Pharmacology in Drug Discovery by : Mithun Rudrapal
Download or read book Biochemical and Molecular Pharmacology in Drug Discovery written by Mithun Rudrapal and published by Elsevier. This book was released on 2024-06-28 with total page 582 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biochemical and Molecular Pharmacology in Drug Discovery comprises fundamental biochemical and molecular aspects of drug discovery and basic understanding of modern drug discovery approaches along with certain key topics related to molecular pharmacology of drugs and therapeutics. Molecular pharmacology has gained significant momentum among researchers, scientists, and academicians because of its increasing interest in drug discovery research across the globe. Molecular pharmacology involves a fundamental understanding of drug actions at the molecular level with the help of several tools and techniques of biochemical and molecular biology. It explains the phenomena of drug-target interactions considering different biochemical systems and cellular strategies. With the advent of technologies, current advances and research trends move toward molecular and/or target-based drug design and discovery. Through this book, readers will be able to gain skills and knowledge with a thorough understanding of the subject of biochemical and molecular pharmacology, in a comprehensive and systematic manner with special reference to recent advances in drug discovery research. Highlights the fundamentals of biochemical and molecular aspects, with reference to drug discovery research Depicts modern drug discovery approaches such as reverse pharmacology, drug repositioning, and CADD in the context of current research updates Summarizes recent developments in the molecular pharmacology of novel drugs/ therapeutic molecules
Book Synopsis A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes by : Sasakthi Senanayaka Abeysinghe
Download or read book A Geometric Approach for Deciphering Protein Structure from Cryo-EM Volumes written by Sasakthi Senanayaka Abeysinghe and published by . This book was released on 2010 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: Electron Cryo-Microscopy or cryo-EM is an area that has received much attention in the recent past. Compared to the traditional methods of X-Ray Crystallography and NMR Spectroscopy, cryo-EM can be used to image much larger complexes, in many different conformations, and under a wide range of biochemical conditions. This is because it does not require the complex to be crystallisable. However, cryo-EM reconstructions are limited to intermediate resolutions, with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure identification. In this dissertation, we present a suite of geometric algorithms to address several aspects of protein modeling using cryo-EM density maps. Specifically, we develop novel methods to capture the shape of density volumes as geometric skeletons. We then use these skeletons to find secondary structure elements (SSEs) of a given protein, to identify the correspondence between these SSEs and those predicted from the primary sequence, and to register high-resolution protein structures onto the density volume. In addition, we designed and developed Gorgon, an interactive molecular modeling system, that integrates the above methods with other interactive routines to generate reliable and accurate protein backbone models.
Book Synopsis Frontiers In Bioimage Informatics Methodology by : Jie Zhou
Download or read book Frontiers In Bioimage Informatics Methodology written by Jie Zhou and published by World Scientific. This book was released on 2024-03-19 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique compendium provides state-of-the-art computational methodology and applications in bioimage informatics. It covers cutting-edge technology developments in biological image analysis, where images come from new modalities and are often large scale, high throughput and high dimensional. The book reflects advances in intelligent algorithms for tasks such as biological image segmentation, reconstruction, and object tracking.Contributed by world renowned researchers, this useful reference text presents case studies that can potentially help readers find approaches and resources to address their imminent scientific problems.
Book Synopsis The Resolution Revolution: Recent Advances In cryoEM by :
Download or read book The Resolution Revolution: Recent Advances In cryoEM written by and published by Academic Press. This book was released on 2016-08-26 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: cryoEM, a new volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods and new developments in recording images, the creation, evaluation and validation of 3D maps from the images, model building into maps and refinement of the resulting atomic structures, and applications of essentially single particle methods to helical structures and to sub-tomogram averaging. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers research methods that determine the structures of biological molecules, a vital step for understanding their function Contains the technical developments underpinning the advances of cryoEM and captures the exciting insights that have resulted
Book Synopsis Ion Channel Structure and Drug Discovery Accelerated by Cryo-EM by : Shujia Zhu
Download or read book Ion Channel Structure and Drug Discovery Accelerated by Cryo-EM written by Shujia Zhu and published by Frontiers Media SA. This book was released on 2022-11-30 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Advances in Protein Molecular and Structural Biology Methods by : Timir Tripathi
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Book Synopsis Algorithms and Methods in Structural Bioinformatics by : Nurit Haspel
Download or read book Algorithms and Methods in Structural Bioinformatics written by Nurit Haspel and published by Springer Nature. This book was released on 2022-09-01 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved. In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.
Book Synopsis Protein Structure Determination from Cryo-electron Microscopy Density Maps by : Yu-Ruei Wang
Download or read book Protein Structure Determination from Cryo-electron Microscopy Density Maps written by Yu-Ruei Wang and published by . This book was released on 2015 with total page 71 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-particle cryo-electron microscopy (cryo-EM) has emerged as a powerful tool in structure determination of macromolecular complexes that are not suitable for crystallographic studies. Recent advances in direct electron detectors and image-processing techniques have allowed cryo-EM to reach near-atomic resolution (3--5 Å) from small particles with low or even no symmetry. However, tools to determine structures from cryo-EM maps have lagged behind. In this dissertation we describe approaches that apply Rosetta high-resolution structure prediction methods to model-building from cryo-EM maps. Using knowledge-based information gathered from proteins of known atomic structure, we describe the development of novel tools for de novo model-building from near-atomic resolution cryo-EM maps, and for architecture determination of multi-component macromolecular assemblies from medium- to low-resolution (5--15 Å) cryo- EM maps. We demonstrate that these new computational tools have shown usefulness in determining the structures from newly reconstructed cryo-EM maps, which would otherwise be difficult or impossible for human to do. These methods should enable rapid and reliable structure determination from cryo-EM maps.
Book Synopsis Enabling Deep Geometric Learning on Cryo-EM Maps Using Neural Representation by : Nathan Ranno
Download or read book Enabling Deep Geometric Learning on Cryo-EM Maps Using Neural Representation written by Nathan Ranno and published by . This book was released on 2021 with total page 44 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to data banks worldwide. Deep geometric learning is intriguing for use in structure segmentation, but the native voxel format of cryo-EM maps is unsuitable as input to such methods. We present a novel data format called the neural cryo-EM map that accurately parameterizes cryo-EM maps and provides native, spatially continuous density and gradient data to serve as the basis for a graph-based interpretation of cryo-EM maps. Density values interpolated using the non-linear neural cryo-EM format are more accurate than conventional tri-linear interpolation. Our graph-based interpretations of 115 experimental cryo-EM maps from 1.15 to 4.0 Angstrom resolution provide high coverage of the underlying amino acid residue locations, while accuracy of nodes is correlated with resolution. The nodes of graphs created from atomic resolution maps (higher than 1.6 Angstrom) provide greater than 99% residue coverage as well as 85% full atomic coverage with a mean of 0.19 Angstrom root mean squared deviation (RMSD). Other graphs have a mean 84% residue coverage with less specificity of the nodes due to experimental noise and differences of density context at lower resolutions. Graphs created from atomic resolution maps may serve as input to downstream deep geometric learning applications and may be generalized to transform any 3D grid-based data format into non-linear, continuous, and differentiable format.
Book Synopsis Explainable AI in Health Informatics by : Rajanikanth Aluvalu
Download or read book Explainable AI in Health Informatics written by Rajanikanth Aluvalu and published by Springer Nature. This book was released on with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Cryo-Electron Microscopy in Structural Biology by : Krishnarao Appasani
Download or read book Cryo-Electron Microscopy in Structural Biology written by Krishnarao Appasani and published by CRC Press. This book was released on 2024-10-17 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-electron microscopy, in combination with tomography, has emerged as a new technology for visualizing molecular structures at a resolution beyond even 1 Å. Using this technology has revealed the native molecular details of viruses, membranes, enzymes, ribosomes, and cells. This comprehensive volume brings together authoritative overviews of these methods from structural and biological perspectives. It is a must-have for researchers and graduate students, as well as those working in industry, primarily in the areas of biophysics, structural biology, crystallography, and genomics. Key Features • Focuses on the applications of cryo-EM to structural biology • Documents the importance of cryo-EM/ET approaches in studying the structural determinants of cellular organelle and membrane protein biochemistry • Reviews the applications of high-resolution structures of viruses • Emphasizes structural insights of nuclear and gene machineries • Includes a section focused entirely on the applications of cryo-EM/ET in drug discovery and therapeutic development
Book Synopsis Efficient Geometric Approaches for Mining Protein Structure from Cryo-EM Density Maps by : Hang Dou
Download or read book Efficient Geometric Approaches for Mining Protein Structure from Cryo-EM Density Maps written by Hang Dou and published by . This book was released on 2017 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt: A protein's 3D structure is the key to understanding its biological function. In recent years, cryo-electron microscopy or cryo-EM has established itself as a mainstream technique to capture proteins' structure at near-native conditions. However the vast majority of cryo-EM data are at medium (5-10A) or low (>10A) resolutions, which is insufficient to capture a protein's atomic structure. Fortunately, at such resolutions, some intrinsic structures of a protein, such as secondary structure elements (SSEs) and smooth c-alpha backbone fragments (SCBFs), can be recognized or robustly detected. In this dissertation, we present efficient protein fitting pipelines to recover a protein's atomic structure given the protein's cryo-EM density map by leveraging the intrinsic structure information detected from the density map. Specifically, we first compute the correspondences between the protein features (SSEs or SCBFs) detected from the cryo-EM density map and those extracted from the template model. Then we fit the template model into the cryo-EM density map guided by the obtained correspondences.
Book Synopsis Protein Complex Structure Determination Guided by Low-resolution Cryo-electron Microscopy Maps by : Daniel P. Farrell
Download or read book Protein Complex Structure Determination Guided by Low-resolution Cryo-electron Microscopy Maps written by Daniel P. Farrell and published by . This book was released on 2021 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4-8 Ã ), with visible secondary structure elements but poorly resolved loops, making model-building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This dissertation describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using Rosetta, and automated EM-map-guided complex assembly. We will show how this method performs on a diverse benchmarking dataset in addition to describing how it was used to build models for three difficult protein complexes that would have been impossible to solve without this software. We anticipate that our approach will be broadly useful for cryoEM structure determination of large complexes containing many subunits for which there are no homologues of known structure.
Book Synopsis Biological Control Systems and Disease Modelling by : Babatunde Ogunnaike
Download or read book Biological Control Systems and Disease Modelling written by Babatunde Ogunnaike and published by Frontiers Media SA. This book was released on 2021-06-04 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt:
