Prediction Of The Extent Of Protein Secondary Structures Using Neural Networks
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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.
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.
Proceedings Of The International Conference On Soft Computing For Problem Solving Socpros 2011 December 20 22 2011
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Author : Kusum Deep
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-04-13
Proceedings Of The International Conference On Soft Computing For Problem Solving Socpros 2011 December 20 22 2011 written by Kusum Deep 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 2012-04-13 with Technology & Engineering categories.
The objective is to provide the latest developments in the area of soft computing. These are the cutting edge technologies that have immense application in various fields. All the papers will undergo the peer review process to maintain the quality of work.
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.
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
Crop Improvement
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Author : Pankaj Kumar
language : en
Publisher: CRC Press
Release Date : 2021-06-29
Crop Improvement written by Pankaj Kumar and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-29 with Science categories.
Crop Improvement: Biotechnological Advances – Biomedical Science The field of biotechnology is advancing at a fast pace. The availability of low-cost DNA/genome sequencing technologies has led to the discovery and functional characterization of myriad of genes imparting stress tolerance and quality traits. The ‘omics’ group of technologies including genomics, proteomics, transcriptomics and metabolomics has revolutionized the agricultural biotechnology sector. The Nobel Prize-winning technology, such as the genome editing technique, is being employed to edit various gene functions in plants aiding in crop improvement. This technology may be adopted very quickly by consumers compared with the transgenic technique because the genome-edited plants have no adverse effects on the genome of the plant itself and on the environment and related species/non-target organisms. In this book, authors have attempted to compile the latest techniques of agricultural biotechnology and their applications in crop improvement. Certain chapters have been dedicated to describe the use of nanotechnology, a fast emerging new technique in the agriculture sector. Features Development, potential and safety issues in biotechnology Advances in genomics, proteomics and transcriptomics in agriculture Protein bioinformatics and its applications Genetically modified (GM) technology and its implications Genome editing in crop improvement Marker-assisted selection (MAS) in crop improvement Mutation breeding Cryobiotechnology Nanotechnology and biosensors This book includes real-world examples and applications making it accessible to a broader interdisciplinary readership. We hope that it will serve as a reference book for researchers engaged in molecular biology and biotechnology and will act as a ready reckoner for postgraduate (PG) students in the biotechnology discipline.
Deep Learning In Science
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Author : Pierre Baldi
language : en
Publisher: Cambridge University Press
Release Date : 2021-07
Deep Learning In Science written by Pierre Baldi and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-07 with Computers categories.
Rigorous treatment of the theory of deep learning from first principles, with applications to beautiful problems in the natural sciences.
Computational Methods
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Author : G.R. Liu
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-05-26
Computational Methods written by G.R. Liu 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 2007-05-26 with Technology & Engineering categories.
The First International Conference on Computational Methods (ICCM04), organized by the department of Mechanical Engineering, National University of Singapore, was held in Singapore, December 15-17, 2004, with great success. This conference proceedings contains some 290 papers from more than 30 countries/regions. The papers cover a broad range of topics such as meshfree particle methods, Generalized FE and Extended FE methods, inverse analysis and optimization methods. Computational methods for geomechanics, machine learning, vibration, shock, impact, health monitoring, material modeling, fracture and damage mechanics, multi-physics and multi-scales simulation, sports and environments are also included. All the papers are pre-reviewed before they are accepted for publication in this proceedings. The proceedings will provide an informative, timely and invaluable resource for engineers and scientists working in the important areas of computational methods.
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.
Bioinformatics Genomics And Proteomics
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Author : Singh Ruchi
language : en
Publisher: Vikas Publishing House
Release Date : 2015
Bioinformatics Genomics And Proteomics written by Singh Ruchi and has been published by Vikas Publishing House this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015 with Technology & Engineering categories.
This is an innovative textbook for undergraduates as well as postgraduates offering basic knowledge of biology. Its aim is to provide state-of-the-art information about this developing science that has the potential to replace existing biological approaches to study genes and proteins. The chapters are explained in a concise yet detailed manner, including ample cross-references, references to literature and databases, tables and illustrations. The book's sound approach to this intricately complex field makes it an exceptional resource for further exploration into biochemistry, molecular biology, genomics and drug designing fields. Abundant learning features make this book the ideal teaching and learning tool. KEY FEATURES • Illustrations to bolster understanding of complex biochemical relations • Tables for quick access to precise data • Extensive end-of-chapter exercises and references • The most basic details furnished for those who are new to biology • User-friendly, Internet-based bioinformatics tools that allow researchers to extract information from databases and analyze it • Analysis of one software tool discussed in each chapter step-by-step from entering the input till interpretation of the results This is an in-depth textbook written for the biologist who wants a thorough understanding of the popular bioinformatics programs and molecular databases currently in use. It provides a broad, application-oriented overview of this technology.