Molecular Docking And Molecular Dynamics

Author : Amalia Stefaniu
Publisher : BoD – Books on Demand
Page : 102 pages
File Size : 55,6 Mb
Release : 2019-12-18
Category : Medical
ISBN : 9781789840919

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Molecular Docking and Molecular Dynamics by Amalia Stefaniu Pdf

This book clearly explains the principles of in silico tools of molecular docking and molecular dynamics. It provides examples of algorithms and procedures proposed by different software programs for visualizing and identifying potential interactions in complexes of biochemical interest. The book is structured in six chapters, each of which discusses different molecular simulation methodologies and provides concrete examples of complexes interactions. In each chapter authors give an overview of the treated subject, a description of the methodologies used, and a discussion of the results. The authors describe computational ways to achieve a rational design of bioactive compounds with various therapeutic applications, including antitumoral agents, antitubercular drugs, nonsteroidal anti-inflammatory drugs, and radiopharmaceuticals.

Author : Alexandre G. De Brevern,Ramanathan Sowdhamini,Agnel Praveen Joseph,Joseph Rebehmed
Publisher : Frontiers Media SA
Page : 201 pages
File Size : 47,6 Mb
Release : 2022-02-24
Category : Science
ISBN : 9782889745098

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Advances in Molecular Docking and Structure-Based Modelling by Alexandre G. De Brevern,Ramanathan Sowdhamini,Agnel Praveen Joseph,Joseph Rebehmed Pdf

Author : K Anand Solomon
Publisher : MJP Publisher
Page : 242 pages
File Size : 43,6 Mb
Release : 2019-06-05
Category : Science
ISBN : 8210379456XXX

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Molecular Modelling and Drug Design by K Anand Solomon Pdf

Molecular modelling is the scientific art of simulating chemicalor biological systems, so that computational methods can beapplied to understand the process concerned. Models usingcomputers are generated using mathematical equations and areevolved based on experimental information that is taken intoconsideration during model building. This book is anintroduction to the field of molecular modelling and drug designin which biological molecules effective in treating diseases arediscovered using in silico methods.

Author : Dimitrios Vlachakis
Publisher : BoD – Books on Demand
Page : 190 pages
File Size : 42,6 Mb
Release : 2018-07-11
Category : Science
ISBN : 9781789233544

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Molecular Docking by Dimitrios Vlachakis Pdf

Molecular docking has always been and will be on the forefront of developments in the eminent field of drug design and medicinal chemistry. At the early days, drug discovery was based on blackboard drawings and expert intuition. However, as times move on, the amount of available information and overall knowledge base that needs to be analyzed cannot be processed manually. This, coupled by the rapid growth in computational infrastructure and processing power, has allowed for the efficient use of molecular docking tools and algorithms to be considered in the greater field of drug discovery. In the postgenomic era, molecular docking has become the key player for the screening of hundreds of thousands of compounds against a repertoire of pharmacological targets.

Author : Mohane S. Coumar
Publisher : Academic Press
Page : 522 pages
File Size : 41,7 Mb
Release : 2021-02-17
Category : Medical
ISBN : 9780128223130

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Molecular Docking for Computer-Aided Drug Design by Mohane S. Coumar Pdf

Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design. The book is divided into three main sections that cover basic techniques, tools, web servers and applications. It is an essential reference for students and researchers involved in drug design and discovery. Covers the latest information and state-of-the-art trends in structure-based drug design methodologies Includes case studies that complement learning Consolidates fundamental concepts and current practice of molecular docking into one convenient resource

Author : Dastmalchi, Siavoush
Publisher : IGI Global
Page : 456 pages
File Size : 50,6 Mb
Release : 2016-05-03
Category : Medical
ISBN : 9781522501169

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Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery by Dastmalchi, Siavoush Pdf

The role of technology in the medical field has resulted in significant developments within the pharmaceutical industry. Computational approaches have emerged as a crucial method in further advancing drug design and development. Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery presents emerging research on the application of computer-assisted design methods for drugs, emphasizing the benefits and improvements that molecular docking has caused within the pharmaceutical industry. Focusing on validation methods, search algorithms, and scoring functions, this book is a pivotal resource for professionals, researchers, students, and practitioners in the field of theoretical and computational chemistry.

Author : Walter Filgueira de Azevedo Jr.
Publisher : Humana
Page : 286 pages
File Size : 54,5 Mb
Release : 2020-08-27
Category : Medical
ISBN : 1493997548

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Docking Screens for Drug Discovery by Walter Filgueira de Azevedo Jr. Pdf

This book focuses on recent developments in docking simulations for target proteins with chapters on specific techniques or applications for docking simulations, including the major docking programs. Additionally, the volume explores the scoring functions developed for the analysis of docking results and to predict ligand-binding affinity as well as the importance of docking simulations for the initial stages of drug discovery. Written for the highly successful Methods in Molecular Biology series, this collection presents the kind of detail and key implementation advice to ensure successful results. Authoritative and practical, Docking Screens for Drug Discovery aims to serve those interested in molecular docking simulation and also in the application of these methodologies for drug discovery.

Author : Management Association, Information Resources
Publisher : IGI Global
Page : 1584 pages
File Size : 48,9 Mb
Release : 2016-12-28
Category : Medical
ISBN : 9781522517634

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Pharmaceutical Sciences: Breakthroughs in Research and Practice by Management Association, Information Resources Pdf

The delivery of optimal pharmaceutical services to patients is a pivotal concern in the healthcare field. By examining current trends and techniques in the industry, processes can be maintained and improved. Pharmaceutical Sciences: Breakthroughs in Research and Practice provides comprehensive coverage of the latest innovations and advancements for pharmaceutical applications. Focusing on emerging drug development techniques and drug delivery for improved health outcomes, this book is ideally designed for medical professionals, pharmacists, researchers, academics, and upper-level students within the growing pharmaceutical industry.

Author : Holger Gohlke
Publisher : John Wiley & Sons
Page : 361 pages
File Size : 43,6 Mb
Release : 2012-05-21
Category : Medical
ISBN : 9783527329663

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Protein-Ligand Interactions by Holger Gohlke Pdf

Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.

Author : Sergio Decherchi,Andrea Cavalli,Pratyush Tiwary,Francesca Grisoni
Publisher : Frontiers Media SA
Page : 119 pages
File Size : 51,7 Mb
Release : 2021-06-08
Category : Science
ISBN : 9782889668632

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Molecular Dynamics and Machine Learning in Drug Discovery by Sergio Decherchi,Andrea Cavalli,Pratyush Tiwary,Francesca Grisoni Pdf

Dr. Sergio Decherchi and Dr. Andrea Cavalli are co-founders of BiKi Technologies s.r.l. - a company that commercializes a Molecular Dynamics-based software suite for drug discovery. All other Topic Editors declare no competing interests with regards to the Research Topic subject.

Author : Dastmalchi, Siavoush
Publisher : IGI Global
Page : 367 pages
File Size : 50,6 Mb
Release : 2016-05-11
Category : Medical
ISBN : 9781522503637

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Applied Case Studies and Solutions in Molecular Docking-Based Drug Design by Dastmalchi, Siavoush Pdf

As the pharmaceutical industry continues to advance, new techniques in drug design are emerging. In order to deliver optimum care to patients, the development of innovative pharmacological techniques has become a widely studied topic. Applied Case Studies and Solutions in Molecular Docking-Based Drug Design is a pivotal reference source for the latest scholarly research on the progress of pharmaceutical design and computational approaches in the field of molecular docking. Highlighting innovative research perspectives and real-world applications, this book is ideally designed for professionals, researchers, practitioners, and medical chemists actively involved in computational chemistry and pharmaceutical sciences.

Author : Francesco L. Gervasio,Vojtech Spiwok,Raimund Mannhold
Publisher : John Wiley & Sons
Page : 420 pages
File Size : 46,7 Mb
Release : 2019-01-04
Category : Medical
ISBN : 9783527806850

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Biomolecular Simulations in Structure-Based Drug Discovery by Francesco L. Gervasio,Vojtech Spiwok,Raimund Mannhold Pdf

A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.

Author : Mark S. Kemp
Publisher : Nova Science Publishers
Page : 184 pages
File Size : 50,7 Mb
Release : 2019
Category : Science
ISBN : 1536160555

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An Introduction to Molecular Dynamics by Mark S. Kemp Pdf

"In the opening chapter of An Introduction to Molecular Dynamics, the method of statistical geometry, based on the construction of a Voronoi polyhedral, is applied to the pattern recognition of atomic environments and to the investigation of the local order in molecular dynamics-simulated materials. Next, the authors discuss the methodology of bimolecular simulations and their advancements, as well as their applications in the field of nanoparticle-biomolecular interactions. The theory of molecular dynamics simulation and some of the recent molecular dynamics methods such as steered molecular dynamics, umbrella sampling, and coarse-grained simulation are also discussed. The use of auxiliary programs in the cases of modified cyclodextrins is discussed. Additionally, results from molecular dynamics studies on cases of inclusion compounds of molecules of different sizes and shapes encapsulated in the same host cyclodextrin have been examined and compared. In closing, the authors discuss the methodology of molecular dynamics simulation with a non-constant force field. In the context of molecular simulations, the term "force field" refers to a set of equations and parameters for the calculation of forces acting on the particles of the system and its potential energy"--

Author : Daan Frenkel,Berend Smit
Publisher : Elsevier
Page : 664 pages
File Size : 44,6 Mb
Release : 2001-10-19
Category : Science
ISBN : 0080519989

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Understanding Molecular Simulation by Daan Frenkel,Berend Smit Pdf

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: · Transition path sampling and diffusive barrier crossing to simulaterare events · Dissipative particle dynamic as a course-grained simulation technique · Novel schemes to compute the long-ranged forces · Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations · Multiple-time step algorithms as an alternative for constraints · Defects in solids · The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules · Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

Author : Martin Zacharias
Publisher : World Scientific
Page : 401 pages
File Size : 55,7 Mb
Release : 2010
Category : Science
ISBN : 9781848163393

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Protein-protein Complexes by Martin Zacharias Pdf

Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.