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Computational Methods For Predicting Post Translational Modification Sites


Computational Methods For Predicting Post Translational Modification Sites
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Computational Methods For Predicting Post Translational Modification Sites


Computational Methods For Predicting Post Translational Modification Sites
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Author : Dukka B. KC
language : en
Publisher: Springer Nature
Release Date : 2022-06-13

Computational Methods For Predicting Post Translational Modification Sites written by Dukka B. KC and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-06-13 with Science categories.


This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge, Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction.



Computational Techniques For Biological Sequence Analysis


Computational Techniques For Biological Sequence Analysis
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Author : Saiyed Umer
language : en
Publisher: CRC Press
Release Date : 2025-06-17

Computational Techniques For Biological Sequence Analysis written by Saiyed Umer and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-06-17 with Computers categories.


This book provides an overview of basic and advanced computational techniques for analyzing and understanding protein, RNA, and DNA sequences. It covers effective computing techniques for DNA and protein classifications, evolutionary and sequence information analysis, evolutionary algorithms, and ensemble algorithms. Furthermore, the book reviews the role of machine learning techniques, artificial intelligence, ensemble learning, and sequence-based features in predicting post-translational modifications in proteins, DNA methylation, and mRNA methylation, along with their functional implications. The book also discusses the prediction of protein–protein and protein–DNA interactions, protein structure, and function using computational methods. It also presents techniques for quantitative analysis of protein–DNA interactions and protein methylation and their involvement in gene regulation. Additionally, the use of nature-inspired algorithms to gain insights into gene regulatory mechanisms and metabolic pathways in human diseases is explored. This book acts as a useful reference for bioinformaticians and computational biologists working in the fields of molecular biology, genomics, and bioinformatics. Key Features: Reviews machine learning techniques for DNA sequence classification and protein structure prediction Discusses genetic algorithms for analyzing multiple sequence alignments and predicting protein–protein interaction sites Explores computational methods for quantitative analysis of protein–DNA interactions Examine the role of nature-inspired algorithms in understanding the gene regulation and metabolic pathways Covers evolutionary algorithms and sequence-based features in predicting post-translational modifications



Protein Supersecondary Structures


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.



Prediction Of Protein Secondary Structure


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.



Algorithmic And Artificial Intelligence Methods For Protein Bioinformatics


Algorithmic And Artificial Intelligence Methods For Protein Bioinformatics
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Author : Yi Pan
language : en
Publisher: John Wiley & Sons
Release Date : 2013-10-07

Algorithmic And Artificial Intelligence Methods For Protein Bioinformatics written by Yi Pan 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 2013-10-07 with Medical categories.


Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.



Large Language Models Llms In Protein Bioinformatics


Large Language Models Llms In Protein Bioinformatics
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Author : Dukka B. KC
language : en
Publisher: Springer Nature
Release Date : 2025-07-02

Large Language Models Llms In Protein Bioinformatics written by Dukka B. KC and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-07-02 with Computers categories.


This book presents a comprehensive collection of methods, resources, and studies that use large language models (LLMs) in the field of protein bioinformatics. Reflecting the swift pace of LLM development today, the volume delves into numerous LLM-based tools to investigate proteins science, from protein language models to the prediction of protein-ligand binding sites. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice to ensure success in future research. Authoritative and practical, Large Language Models (LLMs) in Protein Bioinformatics serves as an ideal guide for scientists seeking to tap into the potential of artificial intelligence in this vital area of biological study.



Computational Resources For Understanding Biomacromolecular Covalent Modifications


Computational Resources For Understanding Biomacromolecular Covalent Modifications
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Author : Dong Xu
language : en
Publisher: Frontiers Media SA
Release Date : 2021-09-14

Computational Resources For Understanding Biomacromolecular Covalent Modifications written by Dong Xu 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 2021-09-14 with Science categories.




Microbial Comparative Genomics And Pangenomics New Tools Approaches And Insights Into Gene And Genome Evolution


Microbial Comparative Genomics And Pangenomics New Tools Approaches And Insights Into Gene And Genome Evolution
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Author : Paulo Jorge Dias
language : en
Publisher: Frontiers Media SA
Release Date : 2024-11-11

Microbial Comparative Genomics And Pangenomics New Tools Approaches And Insights Into Gene And Genome Evolution written by Paulo Jorge Dias 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 2024-11-11 with Science categories.


Comparative Genomics is the field of knowledge dedicated to the analysis and comparison of genes and genomes. The scientific areas comprised in this field include subjects as diverse as (just naming a few): 1) the development of algorithms for the alignment of genes, whole genomes, short- and long sequencing reads, 2) the search for remote sequence similarity, 3) the discovery of motifs and sequence patterns, 4) the identification of gene families, 5) the detection of ortholog/paralog groups, 6) the reconstruction of evolutionary history of the genes, 7) the detection of signs of selective forces exerted over genes and genomes, 8) the reconstruction of ancestral DNA and genome sequences, 9) the detection and analysis of genome synteny, 10) the inference of ancestral gene order, among others. In addition, an important new sub-field of Comparative Genomics has emerged in the last decade, referred to as Pangenomics, making available improved tools to analyze the exponential genomic data accumulating since the development of Second- and Third-Generation Sequencing Technologies.



Plant Proteomic Research 3 0


Plant Proteomic Research 3 0
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Author : Setsuko Komatsu
language : en
Publisher: MDPI
Release Date : 2021-04-29

Plant Proteomic Research 3 0 written by Setsuko Komatsu and has been published by MDPI this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-04-29 with Science categories.


The Special Issue “Plant Proteomics 3.0” was conceived in an attempt to address the recent advancements in as well as limitations of current proteomic techniques and their diverse applications to attain new insights into plant molecular responses to various biotic and abiotic stressors and the molecular bases of other processes. Proteomics’ focus is also related to translational purposes, including food traceability and allergen detection. In addition, bioinformatic techniques are needed for more confident identification, quantitation, data analysis and networking, especially with non-model or orphan plants, including medicinal and meditational plants as well as forest tree species. This Special Issue contains 23 articles, including four reviews and 19 original papers.



Microbial Physiology Genetics And Ecology


Microbial Physiology Genetics And Ecology
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Author : Glen Pierce & Lynn Scott
language : en
Publisher: Scientific e-Resources
Release Date : 2019-04-15

Microbial Physiology Genetics And Ecology written by Glen Pierce & Lynn Scott and has been published by Scientific e-Resources this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-15 with categories.


Microbial Physiology retains the logical, easy-to-follow organization of the previous editions. An introduction to cell structure and synthesis of cell components is provided, followed by detailed discussions of genetics, metabolism, growth, and regulation for anyone wishing to understand the mechanisms underlying cell survival and growth. This comprehensive reference approaches the subject from a modern molecular genetic perspective, incorporating new insights gained from various genome projects. The major objective of this book is to identify and focus attention on those methods and concepts that contribute to an understanding of organismal or genetic persistence. In addition, information about microbial physiology, genetics and ecology contributing to persistence of microorganisms or the measurement of persistence will be discussed. Consequently, there is a great need for more baseline information concerning the ecology of microbes in the natural environment. In determining the underlying risks associated with the release of genetically engineered microorganisms, both the target of risk and the critical exposure level must be identified.