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Author: Publisher: ISBN: Category : Languages : en Pages : 3
Book Description
We proposed to determine the underpinnings of a high-throughput computational infrastructure that would support future efforts in therapeutics against biothreat pathogens. Existing modeling capabilities focus on pathogen detection, but extending such capabilities to high-throughput molecular docking would lead to a proactive method to guide the development of therapeutics. This project will focus on determining the feasibility of extending current databases to accommodate molecular docking. We will also examine the feasibility of massive parallelization of docking algorithms and the utility of docking libraries. Transferring this new technique to a high-performance computing (HPC) platform at LLNL would result in a unique capability not available elsewhere in government or industry. We have accomplished the proposed work defined in this LDRD FS study. (1) We successfully defined the feasibility of using three different small-molecule databases for high-throughput docking, the NCI diversity set, ZINC and the ACD. (2) We analyzed the accuracy and parallelization capabilities of six separate docking programs: DOCK, AutoDock, FlexX, Glide, and eHiTS. Each program is completely amenable to parallel execution. The fastest code was eHiTS, and Glide was the most accurate. (3) Customizing large libraries was cumbersome without the proper software, making the databases a bit difficult to tailor. The ZINC database has some prefiltered versions. (4) Scripts were created for quality and job control functions. Further development is needed for analysis and visualization needs. The successful conclusion of this project enables LLNL to have a high-throughput computational docking capability where we have evaluated the codes to specific docking problems and utilized LLNL's HPC for significant gains in performance. We have established a CRADA with an industrial partner (funded by the National Institutes of Health) that will fully utilize this technology for biodefense therapeutic design and development.
Author: Publisher: ISBN: Category : Languages : en Pages : 3
Book Description
We proposed to determine the underpinnings of a high-throughput computational infrastructure that would support future efforts in therapeutics against biothreat pathogens. Existing modeling capabilities focus on pathogen detection, but extending such capabilities to high-throughput molecular docking would lead to a proactive method to guide the development of therapeutics. This project will focus on determining the feasibility of extending current databases to accommodate molecular docking. We will also examine the feasibility of massive parallelization of docking algorithms and the utility of docking libraries. Transferring this new technique to a high-performance computing (HPC) platform at LLNL would result in a unique capability not available elsewhere in government or industry. We have accomplished the proposed work defined in this LDRD FS study. (1) We successfully defined the feasibility of using three different small-molecule databases for high-throughput docking, the NCI diversity set, ZINC and the ACD. (2) We analyzed the accuracy and parallelization capabilities of six separate docking programs: DOCK, AutoDock, FlexX, Glide, and eHiTS. Each program is completely amenable to parallel execution. The fastest code was eHiTS, and Glide was the most accurate. (3) Customizing large libraries was cumbersome without the proper software, making the databases a bit difficult to tailor. The ZINC database has some prefiltered versions. (4) Scripts were created for quality and job control functions. Further development is needed for analysis and visualization needs. The successful conclusion of this project enables LLNL to have a high-throughput computational docking capability where we have evaluated the codes to specific docking problems and utilized LLNL's HPC for significant gains in performance. We have established a CRADA with an industrial partner (funded by the National Institutes of Health) that will fully utilize this technology for biodefense therapeutic design and development.
Author: Rajani Sharma Publisher: CRC Press ISBN: 1000988708 Category : Medical Languages : en Pages : 478
Book Description
This new book takes an in-depth look at the emerging and prospective field of computational biology and bioinformatics, which possesses the ability to analyze large accumulated biological data collected from sequence analysis of proteins and genes and cell population with an aim to make new predictions pertaining to drug discovery and new biology. The book explains the basic methodology associated with a bioinformatics and computational approach in drug designing. It then goes on to cover the implementation of computational programming, bioinformatics, pharmacophore modeling, biotechnological techniques, and pharmaceutical chemistry in designing drugs. The major advantage of intervention of computer language or programming is to cut down the number of steps and costs in the field of drug designing, reducing the repeating steps and saving time in screening the potent component for drug or vaccine designing. The book describes algorithms used for drug designing and the use of machine learning and AI in drug delivery and disease diagnosis, which are valuable in clinical decision-making. The implementation of robotics in different diseases like stroke, cancer, COVID-19, etc. is also addressed. Topics include machine learning, AI, databases in drug design, molecular docking, bioinformatics tools, target-based drug design, and immunoinformatics, chemoinformatics, and nanoinformatics in drug design. Drug repurposing in drug design in general as well as for specific diseases, including cancer, Alzheimer’s disease, tuberculosis, COVID-19, etc., is also addressed in depth.
Author: William T. Loging Publisher: Cambridge University Press ISBN: 1316538818 Category : Science Languages : en Pages : 255
Book Description
Computational biology drives discovery through its use of high-throughput informatics approaches. This book provides a road map of the current drug development process and how computational biology approaches play a critical role across the entire drug discovery pipeline. Through the use of previously unpublished, real-life case studies the impact of a range of computational approaches are discussed at various phases of the pipeline. Additionally, a focus section provides innovative visualisation approaches, from both the drug discovery process as well as from other fields that utilise large datasets, recognising the increasing use of such technology. Serving the needs of early career and more experienced scientists, this up-to-date reference provides an essential introduction to the process and background of drug discovery, highlighting how computational researchers can contribute to that pipeline.
Author: Daniel L. Young Publisher: John Wiley & Sons ISBN: 0470261234 Category : Medical Languages : en Pages : 398
Book Description
The first book to focus on comprehensive systems biology as applied to drug discovery and development Drawing on real-life examples, Systems Biology in Drug Discovery and Development presents practical applications of systems biology to the multiple phases of drug discovery and development. This book explains how the integration of knowledge from multiple sources, and the models that best represent that integration, inform the drug research processes that are most relevant to the pharmaceutical and biotechnology industries. The first book to focus on comprehensive systems biology and its applications in drug discovery and development, it offers comprehensive and multidisciplinary coverage of all phases of discovery and design, including target identification and validation, lead identification and optimization, and clinical trial design and execution, as well as the complementary systems approaches that make these processes more efficient. It also provides models for applying systems biology to pharmacokinetics, pharmacodynamics, and candidate biomarker identification. Introducing and explaining key methods and technical approaches to the use of comprehensive systems biology on drug development, the book addresses the challenges currently facing the pharmaceutical industry. As a result, it is essential reading for pharmaceutical and biotech scientists, pharmacologists, computational modelers, bioinformaticians, and graduate students in systems biology, pharmaceutical science, and other related fields.
Author: Anton Yuryev Publisher: John Wiley & Sons ISBN: 0470399260 Category : Science Languages : en Pages : 332
Book Description
This book introduces drug researchers to the novel computational approaches of pathway analysis and explains the existing applications that can save time and money in the drug discovery process. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. It explains pathway reconstruction of diseases and toxic states, pathway analysis in various phases, dynamic modeling of drug responses, and more. This is a core resource for drug discovery and pharmaceutical industry researchers, chemists, and biologists and for professionals in related fields.
Author: Richard S. Larson Publisher: ISBN: 9781617799655 Category : Bioinformatics Languages : en Pages : 374
Book Description
Recent advances in drug discovery have been rapid. The second edition of Bioinformatics and Drug Discovery has been completely updated to include topics that range from new technologies in target identification, genomic analysis, cheminformatics, protein analysis, and network or pathway analysis. Each chapter provides an extended introduction that describes the theory and application of the technology. In the second part of each chapter, detailed procedures related to the use of these technologies and software have been incorporated. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Bioinformatics and Drug Discovery, Second Edition seeks to aid scientists in the further study of the rapidly expanding field of drug discovery.
Author: Richard S. Larson Publisher: Humana Press ISBN: 9781493990887 Category : Medical Languages : en Pages : 324
Book Description
This third edition volume expands on the previous editions with new topics that cover drug discovery through translational bioinformatics, informatics, clinical research informatics, as well as clinical informatics. The chapters discuss new methods to study target identification, genome analysis, cheminformatics, protein analysis, and text mining. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials, software workflows, reagents and on-line resources, together with step-by-step, readily reproducible laboratory and computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Bioinformatics and Drug Discovery, Third Edition is a valuable resource for anyone interested in drug design, including academicians (biologists, informaticists and data scientists, chemists, and biochemists), clinicians, and pharmaceutical scientists.
Author: Aman Chandra Kaushik Publisher: Springer ISBN: 3319757326 Category : Computers Languages : en Pages : 66
Book Description
The application of bioinformatics approaches in drug design involves an interdisciplinary array of sophisticated techniques and software tools to elucidate hidden or complex biological data. This work reviews the latest bioinformatics approaches used for drug discovery. The text covers ligand-based and structure-based approaches for computer-aided drug design, 3D pharmacophore modeling, molecular dynamics simulation, the thermodynamics of ligand−receptor and ligand−enzyme association, thermodynamic characterization and optimization, and techniques for computational genomics and proteomics.
Author: John David MacCuish Publisher: CRC Press ISBN: 1439816794 Category : Computers Languages : en Pages : 235
Book Description
With a DVD of color figures, Clustering in Bioinformatics and Drug Discovery provides an expert guide on extracting the most pertinent information from pharmaceutical and biomedical data. It offers a concise overview of common and recent clustering methods used in bioinformatics and drug discovery.Setting the stage for subsequent material, the firs
Author: 
Author: 
Author: William T. Loging
Author: Rajani Sharma
Author: William T. Loging
Author: Daniel L. Young
Author: Anton Yuryev
Author: Richard S. Larson
Author: Richard S. Larson
Author: Aman Chandra Kaushik
Author: John David MacCuish