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Multiscale Approaches to Protein Modeling by Andrzej Kolinski Pdf
The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by Adam Liwo Pdf
This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly by Anonim Pdf
Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro
Author : Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro Publisher : Frontiers Media SA Page : 235 pages File Size : 42,8 Mb Release : 2020-10-27 Category : Science ISBN : 9782889661091
Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by Valentina Tozzini,Giulia Palermo,Matteo Dal Peraro,Alexandre M. J. J. Bonvin,Rommie E. Amaro Pdf
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Functionally Relevant Macromolecular Interactions of Disordered Proteins by Istvan Simon Pdf
Disordered proteins are relatively recent newcomers in protein science. They were first described in detail by Wright and Dyson, in their J. Mol. Biol. paper in 1999. First, it was generally thought for more than a decade that disordered proteins or disordered parts of proteins have different amino acid compositions than folded proteins, and various prediction methods were developed based on this principle. These methods were suitable for distinguishing between the disordered (unstructured) and structured proteins known at that time. In addition, they could predict the site where a folded protein binds to the disordered part of a protein, shaping the latter into a well-defined 3D structure. Recently, however, evidence has emerged for a new type of disordered protein family whose members can undergo coupled folding and binding without the involvement of any folded proteins. Instead, they interact with each other, stabilizing their structure via “mutual synergistic folding” and, surprisingly, they exhibit the same residue composition as the folded protein. Increasingly more examples have been found where disordered proteins interact with non-protein macromolecules, adding to the already large variety of protein–protein interactions. There is also a very new phenomenon when proteins are involved in phase separation, which can represent a weak but functionally important macromolecular interaction. These phenomena are presented and discussed in the chapters of this book.
Prediction of Protein Structures, Functions, and Interactions by Janusz M. Bujnicki Pdf
The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.
Combining Simulations, Theory, and Experiments into Multiscale Models of Biological Events by Fabio Trovato,Peter J. Bond,Joanna Trylska,Peter Guy Wolynes Pdf
Multiscale Modeling for Process Safety Applications by Arnab Chakrabarty,Sam Mannan,Tahir Cagin Pdf
Multiscale Modeling for Process Safety Applications is a new reference demonstrating the implementation of multiscale modeling techniques on process safety applications. It is a valuable resource for readers interested in theoretical simulations and/or computer simulations of hazardous scenarios. As multi-scale modeling is a computational technique for solving problems involving multiple scales, such as how a flammable vapor cloud might behave if ignited, this book provides information on the fundamental topics of toxic, fire, and air explosion modeling, as well as modeling jet and pool fires using computational fluid dynamics. The book goes on to cover nanomaterial toxicity, QPSR analysis on relation of chemical structure to flash point, molecular structure and burning velocity, first principle studies of reactive chemicals, water and air reactive chemicals, and dust explosions. Chemical and process safety professionals, as well as faculty and graduate researchers, will benefit from the detailed coverage provided in this book. Provides the only comprehensive source addressing the use of multiscale modeling in the context of process safety Bridges multiscale modeling with process safety, enabling the reader to understand mapping between problem detail and effective usage of resources Presents an overall picture of addressing safety problems in all levels of modeling and the latest approaches to each in the field Features worked out examples, case studies, and a question bank to aid understanding and involvement for the reader
In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.
Systems and Synthetic Biology by Vikram Singh,Pawan K. Dhar Pdf
This textbook has been conceptualized to provide a detailed description of the various aspects of Systems and Synthetic Biology, keeping the requirements of M.Sc. and Ph.D. students in mind. Also, it is hoped that this book will mentor young scientists who are willing to contribute to this area but do not know from where to begin. The book has been divided into two sections. The first section will deal with systems biology – in terms of the foundational understanding, highlighting issues in biological complexity, methods of analysis and various aspects of modelling. The second section deals with the engineering concepts, design strategies of the biological systems ranging from simple DNA/RNA fragments, switches and oscillators, molecular pathways to a complete synthetic cell will be described. Finally, the book will offer expert opinions in legal, safety, security and social issues to present a well-balanced information both for students and scientists.
Computational Approaches to Protein Dynamics by Monika Fuxreiter Pdf
The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an
