Model Studies in Molecular Recognition PDF Download
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Author: Julius Rebek
Publisher:
ISBN:
Category :
Languages : en
Pages : 7
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Author: Julius Rebek
Publisher:
ISBN:
Category :
Languages : en
Pages : 7
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Book Description
Author: Wanli You
Publisher:
ISBN: 9780355471953
Category : Cheminformatics
Languages : en
Pages : 262
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Book Description
Molecular recognition is fundamentally important in biological chemistry. Nowadays, with the rapid development of computational technology and algorithm, molecular modeling has become a powerful tool in studying molecular recognition, such as exploring molecular interactions and understanding biological dynamic processes, making significant contributions to modern biology and drug discovery. The state-of-the-art techniques of computational chemistry and molecular modeling can be applied to study a wide range of chemical and biological systems of interest. This enables us to study structural details at the atomic level and obtain chemical/biological information which is not available by experimental measurements. This dissertation project focused on modeling the recognition mechanisms of biomolecules and their conjugated ligands. Multiple computational techniques, such as molecular dynamics simulation, enhanced sampling methods and free energy calculation were applied. The model systems included signaling domains (BRCT domain), kinase (p38 kinase), enzyme system (TRPS) and small biomolecular system (cyclodextrin). The details of protein-ligand interactions, including both enthalpic and entropic contribution within protein domain-phosphopeptide systems were investigated, based on which new inhibitors were proposed. Several enhanced sampling methods like accelerated molecular dynamics simulation, pathway search guided by internal motions (PSIM) and umbrella sampling, were applied to explore the dissociation pathway of kinase-ligand systems and the motions of kinase during dissociation process were studied both thermodynamically and kinetically, protein conformational rearrangement was found to differentiate slow and fast unbinding inhibitors, casting light on high efficacy inhibitor design. Furthermore, using full structural molecular modeling, we explored how the position of a single proton can change the overall protein dynamics and further activate or inactivate enzyme catalysis, elucidating the catalytic mechanism of TRPS. In addition, we performed systematically evaluation to the performance of umbrella sampling, investigated the influence of subtle changes in the dissociation pathways and conformational sampling methods that provide the initial conformations, paving way for future improvement of umbrella sampling. This project studies the details of receptor-ligand interaction and provides a more complete picture of molecular recognition.
Author: Jiangang Chen
Publisher:
ISBN:
Category :
Languages : en
Pages : 208
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Author: Anna Feldman-Salit
Publisher:
ISBN:
Category :
Languages : en
Pages : 161
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Author: F. Diederich
Publisher: Springer Science & Business Media
ISBN: 366203574X
Category : Science
Languages : en
Pages : 274
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Book Description
Reasoning in terms of molecular recognition may be traced back to Emil Fischer, who practiced the art of chemistry at Humboldt University in Prussian Berlin a century ago. Today, it is clearly recognized that molecular recognition impacts and determines all life processes. It has become a key research field in both chemistry and biology and the emerging interface of what now is being called "chemical biology". The technological advances derived from this knowledge are particularly important, diverse, and directly evident in the pharmaceutical industry. Under the auspices of the Ernst Schering Research Foundation, a workshop held in Berlin in February 1998 addressed novel basic developments of potential relevance to drug research efforts. A balance of timely research topics in molecular recognition is presented in the lectures delivered by a multidisciplinary international panel of renowned scholars and documented in this volume.
Author: A.D. Buckingham
Publisher: Springer Science & Business Media
ISBN: 9401121680
Category : Science
Languages : en
Pages : 213
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Book Description
The importance of molecular recognition in chemistry and biology is reflected in a recent upsurge in relevant research, promoted in particular by high-profile initiatives in this area in Europe, the USA and Japan. Although molecular recognition is necessarily microscopic in origin, its consequences are de facto macroscopic. Accordingly, a text that starts with intermolecular interactions between simple molecules and builds to a discussion of molecular recognition involving larger scale systems is timely. This book was planned with such a development in mind. The book begins with an elementary but rigorous account of the various types of forces between molecules. Chapter 2 is concerned with the hydrogen bond between pairs of simple molecules in the gas phase, with particular reference to the preferred relative orientation of the pair and the ease with which this can be distorted. This microscopic view continues in chapter 3 wherein the nature of interactions between solute molecules and solvents or between two or more solutes is examined from the experimental standpoint, with various types of spectroscopy providing the probe of the nature of the interactions. Molecular recognition is central to the catalysis of chemical reactions, especially when bonds are to be broken and formed under the severe con straint that a specific configuration is to result, as in the production of enan tiotopically pure compounds. This important topic is considered in chapter 4.
Author: Benedikt Frieg
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Author: Charles R. Watts
Publisher:
ISBN:
Category : Ligand binding (Biochemistry)
Languages : en
Pages : 628
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Author: Roelof Jan Pieters
Publisher:
ISBN:
Category :
Languages : en
Pages : 143
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Book Description
Author: Rebecca Wade
Publisher: MDPI
ISBN: 3038976148
Category : Science
Languages : en
Pages : 220
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Book Description
Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power and structural and biological information of active compounds and potential target molecules. Nowadays, molecular modeling can be considered to be an integral component of the modern drug discovery and development toolbox. Nevertheless, there are still many methodological challenges to be overcome in the application of molecular modeling approaches to drug discovery. The eight original research and five review articles collected in this book provide a snapshot of the state-of-the-art of molecular modeling in drug design, illustrating recent advances and critically discussing important challenges. The topics covered include virtual screening and pharmacophore modelling, chemoinformatic applications of artificial intelligence and machine learning, molecular dynamics simulation and enhanced sampling to investigate contributions of molecular flexibility to drug–receptor interactions, the modeling of drug–receptor solvation, hydrogen bonding and polarization, and drug design against protein–protein interfaces and membrane protein receptors.
