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Modeling Of Protein Ligand Interactions
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Book Synopsis Protein-Ligand Interactions by : Holger Gohlke
Download or read book Protein-Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-05-21 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein-Ligand Interactions and Drug Design by : Flavio Ballante
Download or read book Protein-Ligand Interactions and Drug Design written by Flavio Ballante and published by Humana. This book was released on 2021-03-24 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.
Book Synopsis Protein Interactions: Computational Methods, Analysis And Applications by : M Michael Gromiha
Download or read book Protein Interactions: Computational Methods, Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Book Synopsis Protein-Ligand Interactions by : Hans-Joachim Böhm
Download or read book Protein-Ligand Interactions written by Hans-Joachim Böhm and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lock-and-key principle formulated by Emil Fischer as early as the end of the 19th century has still not lost any of its significance for the life sciences. The basic aspects of ligand-protein interaction may be summarized under the term 'molecular recognition' and concern the specificity as well as stability of ligand binding. Molecular recognition is thus a central topic in the development of active substances, since stability and specificity determine whether a substance can be used as a drug. Nowadays, computer-aided prediction and intelligent molecular design make a large contribution to the constant search for, e. g., improved enzyme inhibitors, and new concepts such as that of pharmacophores are being developed. An up-to-date presentation of an eternally young topic, this book is an indispensable information source for chemists, biochemists and pharmacologists dealing with the binding of ligands to proteins.
Book Synopsis Modeling Protein Ligand Interactions Using Multi-scale Computational Approaches by : Ashini Bolia
Download or read book Modeling Protein Ligand Interactions Using Multi-scale Computational Approaches written by Ashini Bolia and published by . This book was released on 2015 with total page 153 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular docking serves as an important tool in modeling protein-ligand interactions. Most of the docking approaches treat the protein receptor as rigid and move the ligand in the binding pocket through an energy minimization, which is an incorrect approach as proteins are flexible and undergo conformational changes upon ligand binding. However, modeling receptor backbone flexibility in docking is challenging and computationally expensive due to the large conformational space that needs to be sampled. A novel flexible docking approach called BP-Dock (Backbone Perturbation docking) was developed to overcome this challenge. BP-Dock integrates both backbone and side chain conformational changes of a protein through a multi-scale approach. In BP-Dock, the residues along a protein chain are perturbed mimicking the binding induced event, with a small Brownian kick, one at a time. The fluctuation response profile of the chain upon these perturbations is computed by Perturbation Response Scanning (PRS) to generate multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, this approach was applied to a large and diverse dataset of unbound structures as receptors. Furthermore, the protein-peptide docking of PICK1-PDZ proteins was investigated. This study elucidates the determinants of PICK1-PDZ binding that plays crucial roles in numerous neurodegenerative disorders. BP-Dock approach was also extended to the challenging problem of protein-glycan docking and applied to analyze the energetics of glycan recognition in Cyanovirin-N (CVN), a cyanobacterial lectin that inhibits HIV by binding to its highly glycosylated envelope protein gp120. This study provide the energetic contribution of the individual residues lining the binding pocket of CVN and explore the effect of structural flexibility in the hinge region of CVN on glycan binding, which are also verified experimentally. Overall, these successful applications of BP-Dock highlight the importance of modeling backbone flexibility in docking that can have important implications in defining the binding properties of protein-ligand interactions.Finally, an induced fit docking approach called Adaptive BP-Dock is presented that allows both protein and ligand conformational sampling during the docking. Adaptive BP-Dock can provide a faster and efficient docking approach for the virtual screening of novel targets for rational drug design and aid our understanding of protein-ligand interactions.
Book Synopsis Protein-Ligand Interactions by : Mark A. Williams
Download or read book Protein-Ligand Interactions written by Mark A. Williams and published by Humana. This book was released on 2016-11-17 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.
Book Synopsis Applications and Improvements in the Molecular Modeling of Protein and Ligand Interactions by : Jason Bret Harris
Download or read book Applications and Improvements in the Molecular Modeling of Protein and Ligand Interactions written by Jason Bret Harris and published by . This book was released on 2014 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding protein and ligand interactions is fundamental to treat disease and avoid toxicity in biological organisms. Molecular modeling is a helpful but imperfect tool used in computer-aided toxicology and drug discovery. In this work, molecular docking and structural informatics have been integrated with other modeling methods and physical experiments to better understand and improve predictions for protein and ligand interactions. Results presented as part of this research include: 1.) an application of single-protein docking for an intermediate state structure, specifically, modeling an intermediate state structure of alpha-1-antitrypsin and using the resulting model to virtually screen for chemical inhibitors that can treat alpha-1-antitrypsin deficiency, 2.) an application of multi-protein docking and metabolism prediction, specifically, modeling the cytochrome P450 metabolism and estrogen receptor activity of an environmental pollutant (PCB-30), and 3.) providing evidence to support the inclusion of anion-pi interactions in molecular modeling by demonstrating the biological roles of anion-pi interactions in stabilizing protein and protein-ligand structures. This work has direct applications for mitigating disease and toxicity, but it also demonstrates useful ways of integrating computational and experimental data to improve upon modeling protein and ligand interactions.
Book Synopsis Modeling Flexibility in Protein-ligand Recognition by : Mária Ildikó Závodszky
Download or read book Modeling Flexibility in Protein-ligand Recognition written by Mária Ildikó Závodszky and published by . This book was released on 2003 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Techniques for Modeling Protein-ligand Interactions and Their Application to Serine Proteases and Asparaginyl-tRNA Synthetase by : Paul C. Sanschagrin
Download or read book Computational Techniques for Modeling Protein-ligand Interactions and Their Application to Serine Proteases and Asparaginyl-tRNA Synthetase written by Paul C. Sanschagrin and published by . This book was released on 2001 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Modeling of Protein-ligand Interactions by : Olli Pentikäinen
Download or read book Modeling of Protein-ligand Interactions written by Olli Pentikäinen and published by . This book was released on 2003 with total page 43 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :Irena Roterman-Konieczna Publisher :Springer Science & Business Media ISBN 13 :9400752849 Total Pages :173 pages Book Rating :4.4/5 (7 download)
Book Synopsis Identification of Ligand Binding Site and Protein-Protein Interaction Area by : Irena Roterman-Konieczna
Download or read book Identification of Ligand Binding Site and Protein-Protein Interaction Area written by Irena Roterman-Konieczna and published by Springer Science & Business Media. This book was released on 2012-10-19 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task – it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.
Book Synopsis Molecular Modeling of Proteins by : Andreas Kukol
Download or read book Molecular Modeling of Proteins written by Andreas Kukol and published by Humana Press. This book was released on 2017-04-30 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Book Synopsis Protein-ligand Interactions, Structure and Spectroscopy by : Stephen E. Harding
Download or read book Protein-ligand Interactions, Structure and Spectroscopy written by Stephen E. Harding and published by Oxford University Press, USA. This book was released on 2001 with total page 474 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text on protein-ligand interactions offers a selection of the most useful and easily applied methods and acts as a guide to the principal techniques used.
Book Synopsis The Homology Modelling of Protein-ligand Interactions by : James Andrew Rupert Dalton
Download or read book The Homology Modelling of Protein-ligand Interactions written by James Andrew Rupert Dalton and published by . This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Statistical Models of Protein-ligand Interactions and Protein Geometry by : Robert Simon DeWitte
Download or read book Statistical Models of Protein-ligand Interactions and Protein Geometry written by Robert Simon DeWitte and published by . This book was released on 1997 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Conformational Dynamics by : Ke-li Han
Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
Book Synopsis Understanding Protein-ligand Interactions by : Sunil Patel
Download or read book Understanding Protein-ligand Interactions written by Sunil Patel and published by . This book was released on 1998 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt:
