Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Download Monte Carlo Simulations Of Protein Structure And Aggregation full books in PDF, epub, and Kindle. Read online Monte Carlo Simulations Of Protein Structure And Aggregation ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Author :
Publisher :
ISBN 13 :
Total Pages : 76 pages
Book Rating : 4.:/5 (924 download)
Download or read book Monte Carlo Simulations of Protein Structure and Aggregation written by and published by . This book was released on 1996 with total page 76 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Rehman Fazeem
Publisher :
ISBN 13 :
Total Pages : 185 pages
Book Rating : 4.:/5 (87 download)
Download or read book Protein Aggregation at Solid/liquid Interfaces: a Monte Carlo Study with Explicit and Implicit Solvent Effects written by Rehman Fazeem and published by . This book was released on 2013 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Metropolis Monte Carlo (MC) simulations were performed with positively charged peptides in aqueous solution to study changes in peptide conformations at solid/liquid interface, and its effects on protein aggregation. Intermediate-resolution diblock model peptide, comprising of 10 units of ALA (non-polar) and LYS (polar) amino acid residues, was used for the simulations. In the first approach to modeling, solvent effects were considered explicitly. The explicit model was then used to study two peptide molecules, in helical structure, at solid/liquid interface. In order to increase the number of peptide molecules in the simulation box, with reduced computational cost, an implicit solvent model was developed with nonadditive hydrogen bonding and hydrophobic interaction potentials. The implicit model was used to simulate two peptides of helical structure at charged surfaces (to compare with the explicit model), and ten peptides of random coil structure with and without charged surfaces. The peptides were observed to always move towards the negatively charged surface and orient with residues of complimentary charge settling close to the surface, maximizing the electrostatic interactions. On reaching the surface, the peptides partially lose their secondary structure and clusters around the hydrophobic ends; this restructuring and dehydration of the peptides provides the entropic drive for adsorption and subsequent misfolding events. The 2- peptide-water-surface system in explicit model was also simulated with periodic switching of surface charge polarity, to induce a "shaking effect" in order to observe possible peptide configurational changes"--Abstract, page iii.
Author : Kym Denys Eden-Jones
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (89 download)
Download or read book Kinetic Monte Carlo Simulations of Autocatalytic Protein Aggregation written by Kym Denys Eden-Jones and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Mai Suan Li
Publisher : Humana
ISBN 13 : 9781071615454
Total Pages : 478 pages
Book Rating : 4.6/5 (154 download)
Download or read book Computer Simulations of Aggregation of Proteins and Peptides written by Mai Suan Li and published by Humana. This book was released on 2022-02-16 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides computational methods and reviews various aspects of computational studies of protein aggregation. Chapters discuss the relationship between protein misfolding and protein aggregation, methods of prediction of aggregation propensities of protein, peptides, protein structure, results of computer simulations of aggregation, and computational simulations focused on specific diseases such as Alzheimer’s, Parkinson’s, and preeclampsia. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computer Simulations of Aggregation of Proteins and Peptides aims to ensure successful results in the further study of this vital field.
Author : Ying Xu
Publisher : Springer Science & Business Media
ISBN 13 : 0387683720
Total Pages : 408 pages
Book Rating : 4.3/5 (876 download)
Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2007-08-24 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
Author : Vera D. Prytkova
Publisher :
ISBN 13 : 9780355307580
Total Pages : 52 pages
Book Rating : 4.3/5 (75 download)
Download or read book Multi-conformation Monte Carlo written by Vera D. Prytkova and published by . This book was released on 2017 with total page 52 pages. Available in PDF, EPUB and Kindle. Book excerpt: We present a novel multi-conformation Monte Carlo simulation method that enables the modeling of protein-protein interactions and aggregation in crowded protein solutions. This approach is relevant to a molecular-scale description of realistic biological environments, including the cytoplasm and the extracellular matrix, that are characterized by high concentrations of biomolecular solutes (e.g., 300-400 mg/mL for proteins and nucleic acids in the cytoplasm of Escherichia coli). Simulation of such environments necessitates the inclusion of a large number of protein molecules. Therefore, computationally inexpensive methods, such as rigid-body Brownian dynamics or Monte Carlo simulations, can be particularly useful. However, as we demonstrate herein, the rigid-body representation typically employed in simulations of many-protein systems gives rise to certain artifacts in protein-protein interactions. Our approach allows us to incorporate molecular flexibility in Monte Carlo simulations at low computational cost, thereby eliminating ambiguities arising from structure selection in rigid-body simulations. We benchmark and validate the methodology using simulations of hen egg white lysozyme in solution, a well-studied system for which extensive experimental data, including osmotic second virial coefficients, small-angle scattering structure factors, and multiple structures determined by x-ray and neutron crystallography and solution NMR, as well as rigid-body BD simulation results, are available for comparison.
Author : Adam Liwo
Publisher : Springer
ISBN 13 : 3319958437
Total Pages : 851 pages
Book Rating : 4.3/5 (199 download)
Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer. This book was released on 2018-12-19 with total page 851 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Becky Lynn Eggimann
Publisher :
ISBN 13 :
Total Pages : 366 pages
Book Rating : 4.:/5 (319 download)
Download or read book Monte Carlo Simulations for NMR-based Protein Structure Determination, Aqueous Interfacial Properties, and Pressure-volume Curves written by Becky Lynn Eggimann and published by . This book was released on 2006 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computer Simulations of Protein Folding and Aggregation written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer simulation is used to study the competition between protein folding and aggregation, especially the formation of ordered structures that are also known as amyloid fibrils. Employing simplified protein models, we simulate multi-protein systems at a greater level of detail than has previously been possible, probe the fundamental physics that govern protein folding and aggregation, and explore the energetic and structural characteristics of amorphous and fibrillar protein aggregates. We first tackle the aggregation problem by using a low-resolution model called the lattice HP model developed by Lau and Dill. Dynamic Monte Carlo simulations are conducted on a system of simple, two-dimensional lattice protein molecules. We investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of the model protein molecule by simulating three renaturation methods: infinitely slow cooling, slow but finite cooling, and quenching. We find that the infinitely slow cooling method provides the highest refolding yields. We then study how the variation of protein concentration affects the refolding yield by simulating the pulse renaturation method, in which denatured proteins are slowly added to the refolding simulation box in a stepwise manner. We observe that the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods even at high packing fractions. We then investigate the folding of a polyalanine peptide with the sequence Ac-KA14K-NH2 using a novel off-lattice, intermediate-resolution protein model originally developed by Smith and Hall. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule is explored by employing the replica exchange simulation method to map out the conformational transitions as a function of temperature. We also explore the influence of solvent type on the folding process by varying the relative strength of the sid.
Author : Serafin Fraga
Publisher : Springer Science & Business Media
ISBN 13 : 3642514995
Total Pages : 296 pages
Book Rating : 4.6/5 (425 download)
Download or read book Computer Simulations of Protein Structures and Interactions written by Serafin Fraga and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Author :
Publisher :
ISBN 13 : 9789174738117
Total Pages : 31 pages
Book Rating : 4.7/5 (381 download)
Download or read book Protein Aggregation written by and published by . This book was released on 2014 with total page 31 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Yuanwei Xu
Publisher :
ISBN 13 :
Total Pages : 216 pages
Book Rating : 4.:/5 (11 download)
Download or read book Advances in Monte Carlo Techniques with Application to Lattice Protein Aggregation written by Yuanwei Xu and published by . This book was released on 2016 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andrzej Kolinski
Publisher : Springer Science & Business Media
ISBN 13 : 144196889X
Total Pages : 360 pages
Book Rating : 4.4/5 (419 download)
Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : Kristian Dimitrievski
Publisher :
ISBN 13 : 9789162867676
Total Pages : 98 pages
Book Rating : 4.8/5 (676 download)
Download or read book Monte Carlo Simulations of Supported Biomembranes and Protein Folding written by Kristian Dimitrievski and published by . This book was released on 2006 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : George Vasmatzis
Publisher :
ISBN 13 :
Total Pages : 194 pages
Book Rating : 4.:/5 (33 download)
Download or read book Constrained Minimization Using Adaptive Monte Carlo in Protein Structure Determination written by George Vasmatzis and published by . This book was released on 1993 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Aaron Reuven Dinner
Publisher :
ISBN 13 : 9780599368729
Total Pages : 433 pages
Book Rating : 4.3/5 (687 download)
Download or read book Monte Carlo Simulations of Protein Folding written by Aaron Reuven Dinner and published by . This book was released on 1999 with total page 433 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :
Publisher : Academic Press
ISBN 13 : 0128211377
Total Pages : 554 pages
Book Rating : 4.1/5 (282 download)
Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-05 with total page 554 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
