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Determining Alpha Helix Correspondence For Protein Structure Prediction From Cryo Em Density Maps
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Book Synopsis Determining [alpha]-helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps by : Sasakthi Senanayaka Abeysinghe
Download or read book Determining [alpha]-helix Correspondence for Protein Structure Prediction from Cryo-EM Density Maps written by Sasakthi Senanayaka Abeysinghe and published by . This book was released on 2007 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 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 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.
Download or read book Cryo-EM, Part C written by and published by Academic Press. This book was released on 2010-09-30 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume, along with Part A and Part B, is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. Includes time-tested core methods and new innovations applicable to any researcher Methods included are useful to both established researchers and newcomers to the field Relevant background and reference information given for procedures can be used as a guide
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 Structural Bioinformatics of Membrane Proteins by : D. Frishman
Download or read book Structural Bioinformatics of Membrane Proteins written by D. Frishman and published by Springer Science & Business Media. This book was released on 2011-01-22 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is the first one specifically dedicated to the structural bioinformatics of membrane proteins. With a focus on membrane proteins from the perspective of bioinformatics, the present work covers a broad spectrum of topics in evolution, structure, function, and bioinformatics of membrane proteins focusing on the most recent experimental results. Leaders in the field who have recently reported breakthrough advances cover algorithms, databases and their applications to the subject. The increasing number of recently solved membrane protein structures makes the expert coverage presented here very timely. Structural bioinformatics of membrane proteins has been an active area of research over the last thee decades and proves to be a growing field of interest.
Book Synopsis Protein Structure by Distance Analysis by : Henrik Bohr
Download or read book Protein Structure by Distance Analysis written by Henrik Bohr and published by IOS Press. This book was released on 1994 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events by : Fabio Trovato
Download or read book Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events written by Fabio Trovato and published by Frontiers Media SA. This book was released on 2022-01-11 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Structure Prediction by : David Webster
Download or read book Protein Structure Prediction written by David Webster and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.
Book Synopsis Advances in Computer Aided Protein Structure Determination from Sparse Cryo Electron Microscopy Data by : Brandon Frenz
Download or read book Advances in Computer Aided Protein Structure Determination from Sparse Cryo Electron Microscopy Data written by Brandon Frenz and published by . This book was released on 2017 with total page 54 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-particle cryo-electron microscopy (cryoEM) has become a powerful tool for determining macromolecular structures. Thanks to recent advances in direct electron detectors and motion correction algorithms it can frequently deliver electron density maps in the range of 3-5Å resolution. To obtain as much atomic level detail of the structure as possible from this data an accurate atomic model must be built. This can be done manually however, it is laborious and error prone. To resolve this problem modelers have turned to computational tools which can make up for lack of experimental data. Here we describe several tools for modeling with sparse experimental data, including a novel sampling strategy for de novo model completion and a novel refinement strategy for glycans with near atomic resolution cryoEM and x-ray crystallography data.
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 A Graph-based Algorithm to Determine Protein Structure from Cryo-EM Data by : Stephen Schuh
Download or read book A Graph-based Algorithm to Determine Protein Structure from Cryo-EM Data written by Stephen Schuh and published by . This book was released on 2011 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Ab Initio Protein Tertiary Structure Prediction Constrained by Extracted Secondary Structures from CryoEM Density Maps by : Yonggang Lu
Download or read book Ab Initio Protein Tertiary Structure Prediction Constrained by Extracted Secondary Structures from CryoEM Density Maps written by Yonggang Lu and published by . This book was released on 2007 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Alignment Methods Comparison for Fitting Cryo-EM Density Map with Predicted Protein Structures by : Xiaoxiao Qin
Download or read book Alignment Methods Comparison for Fitting Cryo-EM Density Map with Predicted Protein Structures written by Xiaoxiao Qin and published by . This book was released on 2008 with total page 42 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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