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Book
Synthesis of Marine Natural Products and Molecules Inspired by Marine Substances II
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Year: 2021 Publisher: Basel, Switzerland MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

This Special Issue, comprising five articles, describes the synthetic methodologies and biological activity of different classes of bioactive marine metabolites and analogs crucial to favor pharmacological applications of these molecules.


Book
Molecular Modeling in Drug Design
Authors: ---
Year: 2019 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

This book is a printed edition of the Special Issue Molecular Modeling in Drug Design that was published in Molecules

Keywords

metadynamics --- natural compounds --- virtual screening --- probe energies --- molecular dynamics simulation --- human ecto-5?-nucleotidase --- neural networks --- quantitative structure-activity relationship (QSAR) --- artificial intelligence --- allosterism --- in silico screening --- drug discovery --- amyloid fibrils --- mechanical stability --- adenosine receptors --- adenosine receptor --- ligand binding --- promiscuous mechanism --- AutoGrid --- dynamic light scattering --- resultant dipole moment --- density-based clustering --- Alzheimer’s disease --- drug design --- biophenols --- enzymatic assays --- all-atom molecular dynamics simulation --- fragment screening --- adenosine --- docking --- molecular docking --- cosolvent molecular dynamics --- turbidimetry --- squalene synthase (SQS) --- molecular recognition --- protein-peptide interactions --- extracellular loops --- FimH --- binding affinity --- rational drug design --- de novo design --- hyperlipidemia --- AR ligands --- aggregation --- property prediction --- PPI inhibition --- deep learning --- proteins --- quantitative structure-property prediction (QSPR) --- protein protein interactions --- boron cluster --- target-focused pharmacophore modeling --- ligand–protofiber interactions --- structure-based drug design --- scoring function --- grid maps --- solvent effect --- adhesion --- molecular dynamics --- Traditional Chinese Medicine --- steered molecular dynamics --- interaction energy --- EphA2-ephrin A1 --- molecular modeling --- method development


Book
Computational Methods of Multi-Physics Problems
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ISBN: 3039214187 3039214179 Year: 2019 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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This book offers a collection of six papers addressing problems associated with the computational modeling of multi-field problems. Some of the proposed contributions present novel computational techniques, while other topics focus on applying state-of-the-art techniques in order to solve coupled problems in various areas including the prediction of material failure during the lithiation process, which is of major importance in batteries; efficient models for flexoelectricity, which require higher-order continuity; the prediction of composite pipes under thermomechanical conditions; material failure in rock; and computational materials design. The latter exploits nano-scale modeling in order to predict various material properties for two-dimensional materials with applications in, for example, semiconductors. In summary, this book provides a good overview of the computational modeling of different multi-field problems.


Book
Modeling and Experimental Characterization of Nanocomposite Materials
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ISBN: 3039286331 3039286323 Year: 2020 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

This Special Issue gathers research from different branches of science and engineering disciplines working on experiments and modelling of nanocomposites into one volume. The Guest Editor welcomes papers dedicated to experimental, computational, and theoretical aspects dealing with many important state-of-the-art technologies and methodologies regarding the synthesis, fabrication, characterization, properties, design, and applications, and both finite element analysis and molecular dynamic simulations, of nanocomposite materials and structures. Full papers covering novel topics, extending the frontiers of the science and technology of nanoreinforced composites are encouraged. Reviews covering topics of major interest will be also considered.


Book
Transient Changes in Molecular Geometries and How to Model Them : Simulating Chemical Reactions of Metal Complexes in Solution to Explore Dynamics, Solvation, Coherence, and the Link to Experiment
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ISBN: 9783319187471 3319187465 9783319187464 3319187473 Year: 2015 Publisher: Cham : Springer International Publishing : Imprint: Springer,

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Abstract

This thesis examines various aspects of excess excitation energy dissipation via dynamic changes in molecular structure, vibrational modes and solvation. The computational work is carefully described and the results are compared to experimental data obtained using femtosecond spectroscopy and x-ray scattering. The level of agreement between theory and experiment is impressive and provides both a convincing validation of the method and significant new insights into the chemical dynamics and molecular determinants of the experimental data. Hence, the method presented in the thesis has the potential to become a very important contribution to the rapidly growing field of femtosecond x-ray science, a trend reflected in the several free-electron x-ray lasers (XFELs) currently being built around the world.   Light-induced chemical processes are accompanied by molecular motion of electrons and nuclei on the femtosecond time scale. Uncovering these dynamics is central to our understanding of the chemical reaction on a fundamental level.   Asmus O. Dohn has implemented a highly efficient QM/MM Direct Dynamics method for predicting the solvation dynamics of transition metal complexes in solution.


Book
Recent Progress in Solid Dispersion Technology
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ISBN: 3039215027 3039215019 Year: 2019 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Amorphous solid dispersion (ASD) is a powerful formulation technology to improve oral absorption of poorly soluble drugs. Despite their being in existence for more than half a century, controlling ASD performance is still regarded as difficult because of ASD’s natural non-equilibrium. However, recent significant advances in ASD knowledge and technology may enable a much broader use of ASD technology. This Special Issue, which includes 3 reviews and 6 original articles, focuses on recent progresses in ASD technology in hopes of helping to accelerate developmental studies in the pharmaceutical industry. In striving for a deep understanding of ASD non-equilibrium behavior, the Special issue also delves into and makes progress in the theory of soft-matter dynamics.


Book
Advanced Mechanical Modeling of Nanomaterials and Nanostructures
Authors: ---
Year: 2022 Publisher: Basel MDPI Books

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Abstract

This reprint presents a collection of contributions on the application of high-performing computational strategies and enhanced theoretical formulations to solve a wide variety of linear or nonlinear problems in a multiphysical sense, together with different experimental studies.


Book
Modeling and Simulation of Lipid Membranes
Authors: ---
Year: 2022 Publisher: Basel MDPI Books

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Abstract

Cell membranes are complex structures able to contain the main elements of the cell and to protect them from the external surroundings, becoming the most fundamental interface in Biology. The main subject of this book is the study of the structure and characteristics of lipid membranes in a wide variety of environments, ranging from simple phospholipid membranes to complex systems including proteins, peptides, or oncogenes as well as the analysis of the interactions of the membrane components with small molecules and drugs. The scope of this book is to provide recent developments on membrane structure, composition and function by means of theoretical and experimental techniques, some of them combining computer simulations with available data obtained at the laboratory.This Special Issue aims to report brand new key contributions to the field and also to give an overview about the connection between experiments and computer simulations, addressing fundamental aspects and applied research in biological membranes, with particular attention paid to the applications of computer modeling and simulation to medicine.


Book
Protein Conformational Dynamics
Authors: --- ---
ISBN: 331902969X 3319029703 Year: 2014 Publisher: Cham : Springer International Publishing : Imprint: Springer,

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Abstract

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
NMR of proteins and small biomolecules
Authors: ---
ISSN: 14365049 ISBN: 3642289169 3642289177 9783642289163 Year: 2012 Volume: 326 Publisher: Berlin : Springer,

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Abstract

J. L. Stark R. Powers Application of NMR and Molecular Docking in Structure-Based Drug Discovery O. Vinogradova J. Qin NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions K. Chen N. Tjandra The Use of Residual Dipolar Coupling in Studying Proteins by NMR H. Li H. Sun NMR Studies of Metalloproteins R. Ishima Recent Developments in 15N NMR Relaxation Studies that Probe Protein Backbone Dynamics T. Qureshi N. K. Goto Contemporary Methods in Structure Determination of Membrane Proteins by Solution NMR X. Zhao Protein Structure Determination by Solid-State NMR K. H. Sze Q. Wu H. S. Tse G. Zhu Dynamic Nuclear Polarization: New Methodology and Applications.

Keywords

Molecular Structure --- Models, Molecular --- Gene Expression --- Amino Acids, Peptides, and Proteins --- Peptide Biosynthesis --- Computer Simulation --- Spectrum Analysis --- Computing Methodologies --- Biochemical Processes --- Chemistry Techniques, Analytical --- Genetic Processes --- Chemical Phenomena --- Chemicals and Drugs --- Metabolism --- Models, Theoretical --- Biochemical Phenomena --- Investigative Techniques --- Genetic Phenomena --- Chemical Processes --- Phenomena and Processes --- Information Science --- Metabolic Phenomena --- Analytical, Diagnostic and Therapeutic Techniques and Equipment --- Proteins --- Protein Biosynthesis --- Molecular Dynamics Simulation --- Magnetic Resonance Spectroscopy --- Chemistry --- Physical Sciences & Mathematics --- Organic Chemistry --- Biomolecules --- Nuclear magnetic resonance spectroscopy. --- Spectra. --- NMR spectroscopy --- Spectroscopy, NMR --- Spectroscopy, Nuclear magnetic resonance --- Biological molecules --- Chemistry. --- Bioorganic chemistry. --- Proteins. --- Bioorganic Chemistry. --- Protein Science. --- Nuclear spectroscopy --- Knight shift --- Molecules --- Molecular biology --- Biochemistry. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Medical sciences --- Bio-organic chemistry --- Biological organic chemistry --- Biochemistry --- Chemistry, Organic --- Composition --- Proteins . --- Proteids --- Polypeptides --- Proteomics --- Biomolecules - Spectra --- Nuclear magnetic resonance spectroscopy --- Proteins - Spectra

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