New Approaches Of Protein Function Prediction From Protein Interaction Networks
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New Approaches Of Protein Function Prediction From Protein Interaction Networks
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Author : Jingyu Hou
language : en
Publisher: Academic Press
Release Date : 2017-01-13
New Approaches Of Protein Function Prediction From Protein Interaction Networks written by Jingyu Hou and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-01-13 with Mathematics categories.
New Approaches of Protein Function Prediction from Protein Interaction Networks contains the critical aspects of PPI network based protein function prediction, including semantically assessing the reliability of PPI data, measuring the functional similarity between proteins, dynamically selecting prediction domains, predicting functions, and establishing corresponding prediction frameworks. Functional annotation of proteins is vital to biological and clinical research and other applications due to the important roles proteins play in various biological processes. Although the functions of some proteins have been annotated via biological experiments, there are still many proteins whose functions are yet to be annotated due to the limitations of existing methods and the high cost of experiments. To overcome experimental limitations, this book helps users understand the computational approaches that have been rapidly developed for protein function prediction. - Provides innovative approaches and new developments targeting key issues in protein function prediction - Presents heuristic ideas for further research in this challenging area
Protein Protein Interactions
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Author : Krishna Mohan Poluri
language : en
Publisher: Springer Nature
Release Date : 2021-05-19
Protein Protein Interactions written by Krishna Mohan Poluri and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-19 with Science categories.
This book provides a comprehensive overview of the fundamental aspects of protein-protein interactions (PPI), including a detailed account of the energetics and thermodynamics involved in these interactions. It also discusses a number of computational and experimental approaches for the prediction of PPI interactions and reviews their principles, advantages, drawbacks, and the recent developments. Further, it offers structural and mechanistic insights into the formation of protein-protein complexes and maps different PPIs into networks to delineate various pathways that operate at the cellular level. Lastly, it describes computational protein-protein docking techniques and discusses their implications for further experimental research. Given its scope, this book is a valuable resource for students, researchers, scientists, entrepreneurs, and medical/healthcare professionals.
Protein Interaction Networks In Health And Disease
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Author : Spyros Petrakis
language : en
Publisher: Frontiers Media SA
Release Date : 2016-10-19
Protein Interaction Networks In Health And Disease written by Spyros Petrakis 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 2016-10-19 with Genetics categories.
The identification and mapping of protein-protein interactions (PPIs) is a major goal in systems biology. Experimental data are currently produced in large scale using a variety of high-throughput assays in yeast or mammalian systems. Analysis of these data using computational tools leads to the construction of large protein interaction networks, which help researchers identify novel protein functions. However, our current view of protein interaction networks is still limited and there is an active field of research trying to further develop this concept to include important processes: the topology of interactions and their changes in real time, the effects of competition for binding to the same protein region, PPI variation due to alternative splicing or post-translational modifications, etc. In particular, a clinically relevant topic for development of the concept of protein interactions networks is the consideration of mutant isoforms, which may be responsible for a pathological condition. Mutations in proteins may result in loss of normal interactions and appearance of novel abnormal interactions that may affect a protein’s function and biological cycle. This Research Topic presents novel findings and recent achievements in the field of protein interaction networks with a focus on disease. Authors describe methods for the identification and quantification of PPIs, the annotation and analysis of networks, considering PPIs and protein complexes formed by mutant proteins associated with pathological conditions or genetic diseases.
Applications Of Artificial Intelligence Machine Learning And Deep Learning In Plant Breeding
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Author : Maliheh Eftekhari
language : en
Publisher: Frontiers Media SA
Release Date : 2024-05-29
Applications Of Artificial Intelligence Machine Learning And Deep Learning In Plant Breeding written by Maliheh Eftekhari 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 2024-05-29 with Science categories.
Artificial Intelligence (AI) is an extensive concept that can be interpreted as a concentration on designing computer programs to train machines to accomplish functions like or better than hu-mans. An important subset of AI is Machine Learning (ML), in which a computer is provided with the capacity to learn its own patterns instead of the patterns and restrictions set by a human programmer, thus improving from experience. Deep Learning (DL), as a class of ML techniques, employs multilayered neural networks. The application of AI to plant science research is new and has grown significantly in recent years due to developments in calculation power, proficien-cies of hardware, and software progress. AI algorithms try to provide classifications and predic-tions. As applied to plant breeding, particularly omics data, ML as a given AI algorithm tries to translate omics data, which are intricate and include nonlinear interactions, into precise plant breeding. The applications of AI are extending rapidly and enhancing intensely in sophistication owing to the capability of rapid processing of huge and heterogeneous data. The conversion of AI techniques into accurate plant breeding is of great importance and will play a key role in the new era of plant breeding techniques in the coming years, particularly multi-omics data analysis. Advancements in plant breeding mainly depend upon developing statistical methods that harness the complicated data provided by analytical technologies identifying and quantifying genes, transcripts, proteins, metabolites, etc. The systems biology approach used in plant breeding, which integrates genomics, transcriptomics, proteomics, metabolomics, and other omics data, provides a massive amount of information. It is essential to perform accurate statistical analyses and AI methods such as ML and DL as well as optimization techniques to not only achieve an understanding of networks regulation and plant cell functions but develop high-precision models to predict the reaction of new Genetically Modified (GM) plants in special conditions. The constructed models will be of great economic importance, significantly reducing the time, labor, and instrument costs when finding optimized conditions for the bio-exploitation of plants. This Research Topic covers a wide range of studies on artificial intelligence-assisted plant breeding techniques, which contribute to plant biology and plant omics research. The relevant sub-topics include, but are not restricted to, the following: • AI-assisted plant breeding using omics and multi-omics approaches • Applying AI techniques along with multi-omics to recognize novel biomarkers associated with plant biological activities • Constructing up-to-date ML modeling and analyzing methods for dealing with omics data related to different plant growth processes • AI-assisted omics techniques in the plant defense process • Combining AI-assisted omics and multi-omics techniques using plant system biology approaches • Combining bioinformatics tools with AI approaches to analyze plant omics data • Designing cutting-edge workflow and developing innovative AI biology methods for omics data analysis
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.
Systems Biology
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Author : Aleš Prokop
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-08-28
Systems Biology written by Aleš Prokop 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 2013-08-28 with Medical categories.
Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.
Learning And Intelligent Optimization Designing Implementing And Analyzing Effective Heuristics
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Author : Thomas Stützle
language : en
Publisher: Springer
Release Date : 2009-11-27
Learning And Intelligent Optimization Designing Implementing And Analyzing Effective Heuristics written by Thomas Stützle and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-11-27 with Computers categories.
LION 3, the Third International Conference on Learning and Intelligent Op- mizatioN, was held during January 14–18 in Trento, Italy. The LION series of conferences provides a platform for researchers who are interested in the int- section of e?cient optimization techniques and learning. It is aimed at exploring the boundaries and uncharted territories between machine learning, arti?cial intelligence, mathematical programming and algorithms for hard optimization problems. The considerable interest in the topics covered by LION was re?ected by the overwhelming number of 86 submissions, which almost doubled the 48 subm- sions received for LION’s second edition in December 2007. As in the ?rst two editions, the submissions to LION 3 could be in three formats: (a) original novel and unpublished work for publication in the post-conference proceedings, (b) extended abstracts of work-in-progressor a position statement, and (c) recently submitted or published journal articles for oral presentations. The 86 subm- sions received include 72, ten, and four articles for categories (a), (b), and (c), respectively.
Computational Vision And Bio Inspired Computing
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Author : S. Smys
language : en
Publisher: Springer Nature
Release Date : 2022-03-30
Computational Vision And Bio Inspired Computing written by S. Smys and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-30 with Technology & Engineering categories.
This book includes selected papers from the 5th International Conference on Computational Vision and Bio Inspired Computing (ICCVBIC 2021), held in Coimbatore, India, during November 25–26, 2021. This book presents state-of-the-art research innovations in computational vision and bio-inspired techniques. The book reveals the theoretical and practical aspects of bio-inspired computing techniques, like machine learning, sensor-based models, evolutionary optimization and big data modeling and management that make use of effectual computing processes in the bio-inspired systems. It also contributes to the novel research that focuses on developing bio-inspired computing solutions for various domains, such as human–computer interaction, image processing, sensor-based single processing, recommender systems and facial recognition, which play an indispensable part in smart agriculture, smart city, biomedical and business intelligence applications.
Computational Approaches In Molecular Interaction Analysis Predicting Protein Complexes Host Pathogen Interactions And Protein Function From Interactome Data
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Author : Limsoon Wong
language : en
Publisher: World Scientific
Release Date : 2025-02-18
Computational Approaches In Molecular Interaction Analysis Predicting Protein Complexes Host Pathogen Interactions And Protein Function From Interactome Data written by Limsoon Wong and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-02-18 with Science categories.
This book presents a curated collection of research articles from the Journal of Bioinformatics and Computational Biology, highlighting advances in protein-protein interaction-based computational methods for predicting protein complexes, host-pathogen interactions (HPIs), and protein functions. In Part I, it addresses the dynamic challenges of protein complex prediction using innovative techniques like GECA and IPC-RPIN, which integrate network topology, gene expression, and GO annotations to improve accuracy, especially for small complexes. Part II focuses on HPIs, reviewing computational approaches, predictive models, and tools that enhance understanding of infectious diseases, with a particular emphasis on machine learning applications. Part III delves into protein function prediction, employing PPI networks, multi-label methods, and iterative models that account for dynamic interactions. Collectively, these studies provide a comprehensive resource for advancing computational biology and understanding cellular and disease mechanisms.
Industrial Microbiology And Biotechnology
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Author : Pradeep Verma
language : en
Publisher: Springer Nature
Release Date : 2023-07-08
Industrial Microbiology And Biotechnology written by Pradeep Verma and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-07-08 with Science categories.
The second volume of the Book-Industrial Microbiology and Biotechnology covers various emerging concepts in microbial technology which have been developed to harness the potential of the microbes. The book examines the microbes-based products that have widespread applications in various domains i.e., agriculture, biorefinery, bioremediation, pharmaceutical, and medical sectors. It focusses on recent advances and emerging topics such as CRISPR technology, advanced topics of genomics, including functional genomics, metagenomics, metabolomics, and structural and system biology approaches for enhanced production of industrially relevant products. It further gives an insight into the advancement of genetic engineering with special emphasis on value-added products via microalgal systems and their techno-economics analysis and life cycle assessment. The book towards the end presents recent advancements in the use of microbes for the production of industrial relevant enzymes, amino acids, vitamins, and nutraceuticals, on vaccine development and their biomedical applications. The book is an essential source for researchers working in allied fields of microbiology, biotechnology, and bioengineering.