Multiscale Approaches to Protein Modeling
Title | Multiscale Approaches to Protein Modeling PDF eBook |
Author | Andrzej Kolinski |
Publisher | Springer Science & Business Media |
Pages | 360 |
Release | 2010-10-13 |
Genre | Science |
ISBN | 144196889X |
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.
Multiscale Approaches to Protein Modeling
Title | Multiscale Approaches to Protein Modeling PDF eBook |
Author | |
Publisher | |
Pages | 368 |
Release | 2011-07-11 |
Genre | |
ISBN | 9781441968906 |
Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
Title | Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations PDF eBook |
Author | Valentina Tozzini |
Publisher | Frontiers Media SA |
Pages | 235 |
Release | 2020-10-27 |
Genre | Science |
ISBN | 2889661091 |
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.
Mikē Theodōrakē istories
Title | Mikē Theodōrakē istories PDF eBook |
Author | |
Publisher | |
Pages | 112 |
Release | 2005 |
Genre | |
ISBN |
Protein Modelling
Title | Protein Modelling PDF eBook |
Author | Andrew Gamble |
Publisher | Springer |
Pages | 332 |
Release | 2014-11-13 |
Genre | Science |
ISBN | 3319099760 |
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.
Multiscale Modeling of Biological Complexes
Title | Multiscale Modeling of Biological Complexes PDF eBook |
Author | Xiaochuan Zhao |
Publisher | |
Pages | 208 |
Release | 2021 |
Genre | Multiscale modeling |
ISBN |
Simulating protein complexes on large time and length scales is often intractable at the atomistic resolution. To address this challenge, we have developed new approaches to integrate coarse-grained (CG), mixed-resolution (referred to as AACG throughout this dissertation), and all-atom (AA) modeling for different stages in a single molecular simulation. First, we developed a top-down multiscale modeling approach -- a new approach, which combines CG, AACG, and AA modeling -- to simulate peptide self-assembly from monomers. We simulated the initial encounter stage with the CG model, while the further assembly and reorganization stages are simulated with the AACG and AA models. Further, a theory was developed to estimate the optimal simulation length for each stage. Finally, our approach and theory have been successfully validated with three amyloid peptides. which highlight the synergy from models at multiple resolutions. This approach improves the efficiency of simulating of peptide assembly process. Furthermore, it serves as proof of concept that applying flexible resolution during the simulation, to adapt to efficiency or accuracy. Second, we gained proof of principle from simulating five heterodimeric models of two G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-[mu]s timescales. In these simulations of different resolution levels, we observed consistent structural stability, while the AACG and CG models show two- and four-times faster protein diffusion than the AA models, in addition to 4- and 400-fold speedup in the simulation performance. Our findings enable synergy from the combination of AA, AACG, and CG models, which lay the foundation to combine these models in one single simulation. It is also feasible to alternate among different models to represent an efficient solution to investigate complex biophysical systems. To investigation of environmental sensing of histone-like nucleoid-structuring (H-NS) protein, we also apply AA models to simulate H-NS protein at multiple spatial scales. The environmental sensing ability is reflected by residues at binding sites or filaments mechanical properties. With AA simulation of dimers, we investigated potential of the mean force (PMF), to quantitively determine the sensitivity of the environmental change of binding site. The simulation of H-NS tetramers reveals that the site2 rather than site1 takes responsibility for environmental sensing. Through the simulation of H-NS filaments, we were able to reveal the movement of the DNA binding domain, which is sensitive to environmental sensing, also influence the H-NS stability. Then we extended our investigation to H-NS orthologs from different organism. Our findings revealed the adaptive evolution of H-NS in different organism. Our multiscale modeling approaches can be useful tools to simulate biological complexes. We applied different combination of AA, AACG, and CG models of the same system. Our new computational methodology advanced the ability to simulate large systems or long process more efficiently. Our methodology is readily adaptable to other systems, based on the need of sampling, properties of interest, and simulation efficiency. In any circumstances where balance will be reached between efficiency and high-resolution, multiscale modeling would be significantly valuable in molecular modeling.
Computational Approaches to Protein Dynamics
Title | Computational Approaches to Protein Dynamics PDF eBook |
Author | Monika Fuxreiter |
Publisher | CRC Press |
Pages | 458 |
Release | 2014-12-24 |
Genre | Science |
ISBN | 1482297868 |
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