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Author : Ruiquan Ge
Publisher : Frontiers Media SA
ISBN 13 : 2832503950
Total Pages : 146 pages
Book Rating : 4.8/5 (325 download)
Download or read book Machine Learning for Peptide Structure, Function, and Design written by Ruiquan Ge and published by Frontiers Media SA. This book was released on 2022-11-07 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Jianhua Wang
Publisher : Frontiers Media SA
ISBN 13 : 2832514979
Total Pages : 296 pages
Book Rating : 4.8/5 (325 download)
Download or read book Community Series in Antimicrobial Peptides: Molecular Design, Structure Function Relationship and Biosynthesis Optimization written by Jianhua Wang and published by Frontiers Media SA. This book was released on 2023-02-20 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Jianhua Wang
Publisher : Frontiers Media SA
ISBN 13 : 2889760812
Total Pages : 294 pages
Book Rating : 4.8/5 (897 download)
Download or read book Antimicrobial Peptides: Molecular Design, Structure Function Relationship and Biosynthesis Optimization written by Jianhua Wang and published by Frontiers Media SA. This book was released on 2022-05-04 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Tatiana V. Ovchinnikova
Publisher : MDPI
ISBN 13 : 3039215329
Total Pages : 442 pages
Book Rating : 4.0/5 (392 download)
Download or read book Marine Bioactive Peptides: Structure, Function, and Therapeutic Potential written by Tatiana V. Ovchinnikova and published by MDPI. This book was released on 2019-10-25 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Special Issue Book, “Marine Bioactive Peptides: Structure, Function, and Therapeutic Potential" includes up-to-date information regarding bioactive peptides isolated from marine organisms. Marine peptides have been found in various phyla, and their numbers have grown in recent years. These peptides are diverse in structure and possess broad-spectrum activities that have great potential for medical applications. Various marine peptides are evolutionary ancient molecular factors of innate immunity that play a key role in host defense. A plethora of biological activities, including antibacterial, antifungal, antiviral, anticancer, anticoagulant, endotoxin-binding, immune-modulating, etc., make marine peptides an attractive molecular basis for drug design. This Special Issue Book presents new results in the isolation, structural elucidation, functional characterization, and therapeutic potential evaluation of peptides found in marine organisms. Chemical synthesis and biotechnological production of marine peptides and their mimetics is also a focus of this Special Issue Book.
Author : Naozumi Hiranuma
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)
Download or read book Protein Structure Accuracy Prediction with Deep Learning and Its Application to Structure Prediction and Design written by Naozumi Hiranuma and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the rules of protein structure folding has always been one of the central goals in computational biology. Deep learning is gaining popularity in protein machine learning due to its ability to learn complex functions on large amounts of protein geometry data. To help understand the rules of protein folding better, we developed neural networks (DeepAccNet and Pluto) that estimate the error in protein models. In other words, these networks estimate how much a computationally modeled protein structure deviates from its experimentally determined conformation. Approximately two million conformations from 21000 protein sequences located at different local energy minima with a large diversity of errors were sampled and used for training. The network uses 3D convolutions to evaluate local atomic environments followed by 2D convolutions to provide their global contexts and outperforms other methods that similarly predict the accuracy of protein structure models. Overall accuracy predictions for X-ray and cryoEM structures in the PDB correlate with their resolution. The network should be broadly helpful in assessing the accuracy of both predicted structure models and experimentally determined structures and identifying specific regions likely to be in error. The DeepAccNet methods were selected as top-performing methods for the estimation of model accuracy (EMA) category in CASP14. We extended the accuracy prediction models for proteins to more general chemistry by training graph neural networks on a wide variety of protein and non-protein datasets. We showed that the resulting framework (GAAP) successfully estimates the accuracy of non-protein molecules, such as peptides and Protein-DNA complexes. Our results illustrate how deep learning can impact the efficiency and accuracy of large-scale simulations for both modeling and designing of molecules.
Author : Zhixiu Li
Publisher :
ISBN 13 :
Total Pages : 286 pages
Book Rating : 4.:/5 (939 download)
Download or read book Computational Protein Design written by Zhixiu Li and published by . This book was released on 2015 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational protein design aims at designing amino acid sequences that can fold into a target structure and perform a desired function. Many computational design methods have been developed and their applications have been successful during past two decades. However, the success rate of protein design remains too low to be of a useful tool by biochemists whom are not an expert of computational biology. In this dissertation, we first developed novel computational assessment techniques to assess several state-of-the-art computational techniques. We found that significant progresses were made in several important measures by two new scoring functions from RosettaDesign and from OSCAR-design, respectively. We also developed the first machine-learning technique called SPIN that predicts a sequence profile compatible to a given structure with a novel nonlocal energy-based feature. The accuracy of predicted sequences is comparable to RosettaDesign in term of sequence identity to wild type sequences. In the last two application chapters, we have designed self-inhibitory peptides of Escherichia coli methionine aminopeptidase (EcMetAP) and de novo designed barstar. Several peptides were confirmed inhibition of EcMetAP at the micromole-range 50% inhibitory concentration. Meanwhile, the assessment of designed barstar sequences indicates the improvement of OSCAR-design over RosettaDesign.
Author : John F. Kolen
Publisher : John Wiley & Sons
ISBN 13 : 9780780353695
Total Pages : 458 pages
Book Rating : 4.3/5 (536 download)
Download or read book A Field Guide to Dynamical Recurrent Networks written by John F. Kolen and published by John Wiley & Sons. This book was released on 2001-01-15 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: Acquire the tools for understanding new architectures and algorithms of dynamical recurrent networks (DRNs) from this valuable field guide, which documents recent forays into artificial intelligence, control theory, and connectionism. This unbiased introduction to DRNs and their application to time-series problems (such as classification and prediction) provides a comprehensive overview of the recent explosion of leading research in this prolific field. A Field Guide to Dynamical Recurrent Networks emphasizes the issues driving the development of this class of network structures. It provides a solid foundation in DRN systems theory and practice using consistent notation and terminology. Theoretical presentations are supplemented with applications ranging from cognitive modeling to financial forecasting. A Field Guide to Dynamical Recurrent Networks will enable engineers, research scientists, academics, and graduate students to apply DRNs to various real-world problems and learn about different areas of active research. It provides both state-of-the-art information and a road map to the future of cutting-edge dynamical recurrent networks.
Author : Timir Tripathi
Publisher : Academic Press
ISBN 13 : 0323902650
Total Pages : 716 pages
Book Rating : 4.3/5 (239 download)
Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins
Author : Ilan Samish
Publisher : Humana
ISBN 13 : 9781493966356
Total Pages : 0 pages
Book Rating : 4.9/5 (663 download)
Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Author : Zhibin Lv
Publisher : Frontiers Media SA
ISBN 13 : 2889715558
Total Pages : 112 pages
Book Rating : 4.8/5 (897 download)
Download or read book Feature Representation and Learning Methods With Applications in Protein Secondary Structure written by Zhibin Lv and published by Frontiers Media SA. This book was released on 2021-10-25 with total page 112 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Laszlo Otvos
Publisher : Humana Press
ISBN 13 : 9781617378690
Total Pages : 0 pages
Book Rating : 4.3/5 (786 download)
Download or read book Peptide-Based Drug Design written by Laszlo Otvos and published by Humana Press. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to their high specificity and low toxicity profile, peptides have once again become central to the development of new drugs. In Peptide-Based Drug Design: Methods and Protocols, expert researchers provide a handbook which offers a selection of research and production tools suitable for transforming a promising protein fragment or stand-alone native peptide into a pharmaceutically acceptable composition. The volume delves into contemporary, cutting-edge subjects such as hit isolation and target validation, computer-aided design, sequence modifications to satisfy pharmacologists, in vivo stability and imaging, and the actual production of difficult sequences. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include readily reproducible, step-by-step laboratory protocols, lists of materials, and the Notes section, which highlights tips on troubleshooting and avoiding known pitfalls. Comprehensive and up-to-date, Peptide-Based Drug Design: Methods and Protocols shows its subject to be an independent science on the rise, and provides scientists with a clear, concise guide for continuing this vital research.
Author : Alejandro Speck-Planche
Publisher : Elsevier
ISBN 13 : 9780081011294
Total Pages : 0 pages
Book Rating : 4.0/5 (112 download)
Download or read book Multi-Scale Approaches in Drug Discovery written by Alejandro Speck-Planche and published by Elsevier. This book was released on 2017-03-07 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drug discovery is an expensive, time-consuming process and the modern drug discovery community is constantly challenged not only with discovering novel bioactive agents to combat resistance from known diseases and fight against new ones, but to do so in a way that is economically effective. Advances in both experimental and theoretical/computational methods envisage that the greatest challenges in drug discovery can be most successfully addressed by using a multi-scale approach, drawing on the specialties of a whole host of different disciplines. Multi-Scale Approaches to Drug Discovery furnishes chemists with the detail they need to identify drug leads with the highest potential before isolating and synthesizing them to produce effective drugs with greater swiftness than classical methods may allow. This significantly speeds up the search for more efficient therapeutic agents. After an introduction to multi-scale approaches outlining the need for and benefits of their use, the book goes on to explore a range of useful techniques and research areas, and their potential applications to this process. Profiling drug binding by thermodynamics, machine learning for predicting enzyme sub-classes, and multitasking models for computer-aided design and virtual compound screening are discussed, before the book goes on to review Alkaloid Menispermaceae leads, natural chemotherapeutic agents and methods for speeding up the design and virtual screening of therapeutic peptides. Flavonoids as multi-target compounds are then explored, before the book concludes with a review of Quasi-SMILES as a novel tool. Collecting together reviews and original research contributions written by leading experts in the field, Multi-Scale Approaches to Drug Discovery highlights cutting-edge approaches and practical examples of their implementation for those involved in the drug discovery process at many different levels. Using the combined knowledge of medicinal, computational, pharmaceutical and bio- chemists, it aims to support growth in the multi-scale approach to promote greater success in the development of new drugs.
Author : Knud Jensen
Publisher : John Wiley & Sons
ISBN 13 : 9780470749715
Total Pages : 306 pages
Book Rating : 4.7/5 (497 download)
Download or read book Peptide and Protein Design for Biopharmaceutical Applications written by Knud Jensen and published by John Wiley & Sons. This book was released on 2009-09-01 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Peptides serve as effective drugs in the clinic today. However the inherent drawbacks of peptide structures can limit their efficacy as drugs. To overcome this researchers are developing new methods to create ‘tailor-made’ peptides and proteins with improved pharmacological properties. Design of Peptides and Proteins provides an overview of the experimental and computational methods for peptide and protein design, with an emphasis on specific applications for therapeutics and biomedical research. Topics covered include: Computer modeling of peptides and proteins Peptidomimetics Design and synthesis of cyclic peptides Carbohydrates in peptide and protein design De novo design of peptides and proteins Medical development applications An extended case study – the design of insulin variants Design of Peptides and Proteins presents the state-of-the-art of this exciting approach for therapeutics, with contributions from international experts. It is an essential resource for academic and industrial scientists in the fields of peptide and protein drug design, biomedicine, biochemistry, biophysics, molecular modelling, synthetic organic chemistry and medicinal/pharmaceutical chemistry.
Author :
Publisher : Academic Press
ISBN 13 : 0128054344
Total Pages : 686 pages
Book Rating : 4.1/5 (28 download)
Download or read book Peptide, Protein and Enzyme Design written by and published by Academic Press. This book was released on 2016-08-27 with total page 686 pages. Available in PDF, EPUB and Kindle. Book excerpt: De Novo Enzyme Design, the newest 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 includes the design of metal binding maquettes, insertion of non-natural cofactors, Cu metallopeptides, non-covalent interactions in peptide assemblies, peptide binding and bundling, heteronuclear metalloenzymes, florinated peptides, De Novo imaging agents, and protein-protein interaction. Continues the legacy of this premier serial with quality chapters on de novo enzyme design Represents the newest volume in the Methods in Enzymology series, providing premier, quality chapters authored by leaders in the field Ideal reference for those interested in the study of enzyme design that looks at both structure and mechanism
Author : Renzhi Cao
Publisher :
ISBN 13 :
Total Pages : 169 pages
Book Rating : 4.:/5 (987 download)
Download or read book Genome Data Analysis, Protein Function and Structure Prediction by Machine Learning Techniques written by Renzhi Cao and published by . This book was released on 2016 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt: The raw information of a typical human genome has been generated at 2001 by Human Genome Project. However, since there are a huge amount of data, it is still a big challenge for people to understand them, and extract useful structure and function information, such as the function of genes, the structure of proteins encoded by gene, and the function of proteins. Understanding these information is crucial for us to improve longevity and quality of life, and has a lot of applications, such as genomic medicine, drug design, and etc. In the meantime, machine learning techniques are growing rapidly and are good at processing large datasets, but many of them are limited for the impact on larger real world problems. In this thesis, three major contributions are described. First of all, we generate gene-gene interaction network from human genome conformation data by Hi-C technique, and the relationship of gene function and gene-gene interaction has been discovered. Second, we introduce a novel framework SMISS, which uses new source of information from gene-gene interaction network and uses a new way to integrate difference sources of information for protein function prediction. Finally, we introduce a tool called DeepQA which use machine learning technique to evaluate how well is the predicted protein structure, and a method MULTICOM for protein structure prediction. All of these protein structure and function prediction methods are available as software and web servers which are freely available to the scientific communities.
Author : Katsumi Matsuzaki
Publisher : Springer
ISBN 13 : 9811335885
Total Pages : 304 pages
Book Rating : 4.8/5 (113 download)
Download or read book Antimicrobial Peptides written by Katsumi Matsuzaki and published by Springer. This book was released on 2019-04-12 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of antimicrobial peptides (AMPs), their mechanisms of antimicrobial action, other activities, and various problems that must still be overcome regarding their clinical application. Divided into four major parts, the book begins with a general overview of AMPs (Part I), and subsequently discusses the various mechanisms of antimicrobial action and methods for researching them (Part 2). It then addresses a range of activities other than antimicrobial action, such as cell penetration, antisepsis, anticancer, and immunomodulatory activities (Part 3), and explores the prospects of clinical application from various standpoints such as the selective toxicity, design, and discovery of AMPs (Part 4). A huge number of AMPs have been discovered in plants, insects, and vertebrates including humans, and constitute host defense systems against invading pathogenic microorganisms. Consequently, many attempts have been made to utilize AMPs as antibiotics. AMPs could help to solve the urgent problem of drug-resistant bacteria, and are also promising with regard to sepsis and cancer therapy. Gathering a wealth of information, this book will be a bible for all those seeking to develop antibiotics, anti-sepsis, or anticancer agents based on AMPs.
Author : Glenn King
Publisher : Royal Society of Chemistry
ISBN 13 : 1849736634
Total Pages : 338 pages
Book Rating : 4.8/5 (497 download)
Download or read book Venoms to Drugs written by Glenn King and published by Royal Society of Chemistry. This book was released on 2015-02-11 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book will provide an up to date and comprehensive account of the potential of peptides and proteins from animal venoms as possible therapeutics. The pharmaceutical industry has become increasingly interested in biologics from animal venoms as a potential source for therapeutic agents in recent years, with a particularly emphasis on peptides. To date six drugs derived from venom peptides or proteins have been approved by the FDA, with nine further agents currently being investigated in clinical trials. In addition to these drugs in approved or advanced stages of development, many more peptides and proteins are being studied in varying stages of preclinical development. Topics covered include chemistry and structural biology of animal venoms, proteomic and transcriptomic approaches to drug discovery, bioassays, high-throughput screens and target identification, and reptile, scorpion, spider and cone snail venoms as a platform for drug development. Case studies are used to illustrate methods and successes and highlight issues surrounding administration and other important lessons that have been learnt from the development of approved therapeutics based on venoms. The first text to focus on this fascinating area and bridging an important gap, this book will provide the reader with essential and current knowledge on this fast-developing area. Venoms to Drugs will find wide readership with researchers working in academia and industry working in all medicinal and pharmaceutical areas.
