Prediction Of Protein Secondary Structure
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Prediction Of Protein Secondary Structure
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Author : Andrzej Kloczkowski
language : en
Publisher: Springer Nature
Release Date : 2024-11-22
Prediction Of Protein Secondary Structure written by Andrzej Kloczkowski and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-22 with Science categories.
This second edition volume expands on the previous edition with updates on the latest methods, resources, and studies concerning analysis and prediction of various structural and functional aspects of proteins and ncRNAs. The chapters in this book cover topics such as secondary structure characterization and prediction; the use and impact of AI (including AlphaFold, large language models, and deep neural networks) in the protein structure prediction field; methods and resources for the prediction of posttranslational modifications, residue-residue contacts, subcellular localization, intrinsic disorder, protein-ligand interactions, and protein aggregation; analysis of cryo-EM data; and analysis of noncoding RNAs in the context of human diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions and surveys of the respective topics, list the necessary materials and methods, cover step-by-step instructions on how to use predictive tools and interpret their results, and provide tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Prediction of Protein Secondary Structure, Second Edition is a valuable resource for anyone interested in understanding the dynamic and growing field of the protein structure prediction.
Prediction Of Protein Structures Functions And Interactions
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Author : Janusz M. Bujnicki
language : en
Publisher: John Wiley & Sons
Release Date : 2008-12-23
Prediction Of Protein Structures Functions And Interactions written by Janusz M. Bujnicki and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-12-23 with Science categories.
The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.
Introduction To Protein Structure Prediction
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Author : Huzefa Rangwala
language : en
Publisher: John Wiley & Sons
Release Date : 2011-03-16
Introduction To Protein Structure Prediction written by Huzefa Rangwala and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-03-16 with Science categories.
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.
Prediction Of The Extent Of Protein Secondary Structures Using Neural Networks
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Author : Jurairat Phromjai
language : en
Publisher:
Release Date : 1998
Prediction Of The Extent Of Protein Secondary Structures Using Neural Networks written by Jurairat Phromjai and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998 with Amino acids categories.
We present a method for predicting protein structures based on a digital computer of neural networks. The neural networks learned from existing protein how to predict the secondary structure of amino acid sequences. The amino acid properties of amino acids such as hydropathy, hydrophobicity, helical tendencies and amino acid side chain properties were used as input vector. These properties were coded into the amino acid sequences and used as input patterns for both training and testing. Seventy amino acid sequences and twenty-eight amino acid sequences from different proteins were used for training and testing respectively. The percent predictions accuracies of the existence of helix, sheet and turn structures using in the same network were lower than the prediction from separate networks. Each property gave the highest prediction accuracies for helix structure prediction. Properties can be ranked by their abilities to predict protein secondary structures as follow: (1.1) Amino acid side chain properties gave the highest accuracy for the prediction of the existence of helix, sheet turn in the same network, the existence of sheet and turn structure, percent helix, sheet (3 groups) and percent helix (2 groups). (1.2) Hydropathy (2 groups) gave the highest accuracy for the prediction of the existence of helix structure, percent helix and percent sheet (6 groups), percent turn (3 groups) and percent sheet (2 groups). (2) Hydropathy (7 groups) gave the highest accuracy for the prediction of percent sheet and turn (6 groups) and percent sheet (3 groups). (3) Hydrophobicity gave the highest accuracy for the prediction of percent helix (2 groups). The range of percent accuracy prediction from all properties for helix, sheet and turn were between 85-100%, 70-85% and 45-70% respectively. The range of percent accuracy from all properties for predictions of percent helix, sheet and turn (6 groups of 0%, 1-20%, 21-40%, 41-60%, 61-80% and 81-100%) were 35-65%, 30-50% and 25-50% respectively. Teh percent accuracies for percent helix, sheet and turn (3 groups of 0%, 1-50% and 51-100%) were 65-85%, 60-80% and 50-65% respectively. The percent accuracies for percent helix and sheet (2 groups of 15% and 15%) were 60-80% and 60-75% respectively. The percent of secondary structure prediction is useful for the folding classes prediction.
Protein Structure Prediction
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Author : David Webster
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-02-03
Protein Structure Prediction written by David Webster and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-02-03 with Science categories.
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.
Feature Representation And Learning Methods With Applications In Protein Secondary Structure
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Author : Zhibin Lv
language : en
Publisher: Frontiers Media SA
Release Date : 2021-10-25
Feature Representation And Learning Methods With Applications In Protein Secondary Structure written by Zhibin Lv and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-25 with Science categories.
Protein Supersecondary Structures
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Author : Alexander E. Kister
language : en
Publisher: Springer Nature
Release Date : 2024-11-14
Protein Supersecondary Structures written by Alexander E. Kister and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-14 with Science categories.
This new edition delves into the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Beyond the tremendous advances in the field from the AI-based AlphaFold algorithm, researchers continue to untangle how specific structures and protein folds come to be, and these chapters contain numerous techniques to further pursue this study. Written for the highly successful Methods in Molecular Biology series, chapters contain the kind of detailed implementation advice needed to ensure effective results in the lab. Authoritative and practical, Protein Supersecondary Structures: Methods and Protocols, Third Edition serves as a valuable resource for researchers exploring the relationship between amino acids sequences and protein structures, the evolution of proteins, and the dynamics of protein formation.
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-08-24
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-08-24 with Science categories.
Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
Handbook Of Neural Computation
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Author : E Fiesler
language : en
Publisher: CRC Press
Release Date : 2020-01-15
Handbook Of Neural Computation written by E Fiesler and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-01-15 with Computers categories.
The Handbook of Neural Computation is a practical, hands-on guide to the design and implementation of neural networks used by scientists and engineers to tackle difficult and/or time-consuming problems. The handbook bridges an information pathway between scientists and engineers in different disciplines who apply neural networks to similar probl
Protein Structure
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Author : Daniel Chasman
language : en
Publisher: CRC Press
Release Date : 2003-03-18
Protein Structure written by Daniel Chasman and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2003-03-18 with Medical categories.
This text offers in-depth perspectives on every aspect of protein structure identification, assessment, characterization, and utilization, for a clear understanding of the diversity of protein shapes, variations in protein function, and structure-based drug design. The authors cover numerous high-throughput technologies as well as computational met