作者: 背信 時間: 2025-3-22 00:19 作者: 束以馬具 時間: 2025-3-22 04:04 作者: 遣返回國 時間: 2025-3-22 07:34 作者: Microgram 時間: 2025-3-22 09:10
Book 2013es, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, .Biomolecular Simulations: Method作者: Rejuvenate 時間: 2025-3-22 16:21 作者: 不能根除 時間: 2025-3-22 18:20
Enhanced Sampling Algorithmsand replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present various extensions of these three generalized-ensemble algorithms. The effectiveness of the methods is tested with short peptide and protein systems.作者: 大包裹 時間: 2025-3-22 21:28 作者: Aerophagia 時間: 2025-3-23 05:21
Simulation Studies of the Mechanism of Membrane Transportersall membrane transporters use the widely-accepted “alternating access mechanism,” which ensures that the substrate is only accessible from one side of the membrane at a given time, but relies on complex and usually global protein conformational changes that differ for each family of membrane transpo作者: AV-node 時間: 2025-3-23 05:44 作者: MORPH 時間: 2025-3-23 12:22 作者: 相互影響 時間: 2025-3-23 14:06 作者: Hangar 時間: 2025-3-23 18:23 作者: 縱欲 時間: 2025-3-23 23:35
LBM-LES in an Isothermal Indoor Flow Problemtories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.作者: Metamorphosis 時間: 2025-3-24 03:30
https://doi.org/10.1007/978-0-387-87809-6omings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.作者: 修改 時間: 2025-3-24 08:19 作者: enlist 時間: 2025-3-24 14:15 作者: Spongy-Bone 時間: 2025-3-24 16:46
An Introduction to Best Practices in Free Energy Calculationshem for the first time. We include a variety of examples and tips for how to set up and conduct these calculations, including applications to relative binding affinities and small-molecule solvation free energies.作者: 環(huán)形 時間: 2025-3-24 22:21
Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do Itn itself. Most of the tasks described here are performed using the Gromacs simulation suite, a widely used software for molecular modeling and simulations. In the selected example the attention is focused on a single component lipid bilayer composed of DPPC, one of the most studied lipid species.作者: 溫和女人 時間: 2025-3-25 01:59
Simulating DNA by Molecular Dynamics: Aims, Methods, and Validationtories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.作者: padding 時間: 2025-3-25 06:26 作者: arterioles 時間: 2025-3-25 07:45 作者: 消毒 時間: 2025-3-25 13:15
Fatma Alibaz-Oner,Haner Direskeneli particle-method particle-method Ewald algorithms, multigrid, fast multipole, and local methods. We also highlight some recent developments targeting more accurate, yet classical, representation of the molecular charge distribution.作者: Obligatory 時間: 2025-3-25 19:19 作者: 青石板 時間: 2025-3-25 21:16
Force Fields for Classical Molecular Dynamics introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization philosophies are then presented, followed by a section on force field validation. We conclude with a brief overview on future perspectives for the development of classical force fields.作者: 明智的人 時間: 2025-3-26 03:43 作者: Orchiectomy 時間: 2025-3-26 07:56 作者: 鉤針織物 時間: 2025-3-26 09:30 作者: AMITY 時間: 2025-3-26 15:08 作者: 注意力集中 時間: 2025-3-26 19:18 作者: fidelity 時間: 2025-3-26 22:42 作者: Distribution 時間: 2025-3-27 04:13
QM and QM/MM Simulations of Proteinse field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on larg作者: 正式演說 時間: 2025-3-27 07:20 作者: Precursor 時間: 2025-3-27 10:01
Enhanced Sampling Algorithmsrge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble perform作者: 山間窄路 時間: 2025-3-27 16:55 作者: 音的強弱 時間: 2025-3-27 20:24
Polarizable Force Fieldsorce fields: the induced point dipole, shell, and fluctuating charge models. The importance of including polarization effects in biomolecular simulations is discussed, and some of the most important achievements in the development of polarizable biomolecular force fields to date are highlighted.作者: DRAFT 時間: 2025-3-27 22:05 作者: 一加就噴出 時間: 2025-3-28 05:15 作者: FEIGN 時間: 2025-3-28 09:26
Recipes for Free Energy Calculations in Biomolecular Systemsfined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not trivial as they require knowledge of the methods, insight into the system under study, an作者: Accede 時間: 2025-3-28 10:51
Molecular Docking Methodologiesthe most favorable ligand–target spatial configuration and an estimate of the corresponding complex free energy, although as stated at the beginning accurate scoring methods remain still elusive. In this chapter, the state of art of molecular docking methodologies and their applications in drug disc作者: crucial 時間: 2025-3-28 15:16
Simulation Studies of the Mechanism of Membrane Transportersough coupling the process to various sources of cellular energy, for example, ATP binding and hydrolysis in primary transporters, and pre-established electrochemical gradient of molecular species other than the substrate in the case of secondary transporters. In order to provide efficient energy-cou作者: 燕麥 時間: 2025-3-28 19:53
Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do Itor tool as it grant access to atomic level features of the membrane difficult to access by experimental means. In this chapter we describe step by step how to simulate a membrane .. The explanation comprehends from the initial set up of a membrane system to its analysis passing through the simulatio作者: Albinism 時間: 2025-3-28 23:37 作者: conformity 時間: 2025-3-29 07:05
Simulating DNA by Molecular Dynamics: Aims, Methods, and Validationcharacterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajec作者: 含糊 時間: 2025-3-29 09:50 作者: 結(jié)果 時間: 2025-3-29 12:34
978-1-4939-5891-7Springer Science+Business Media New York 2013作者: Kaleidoscope 時間: 2025-3-29 15:32 作者: BARGE 時間: 2025-3-29 19:46
Methods in Molecular Biologyhttp://image.papertrans.cn/b/image/188259.jpg作者: 動物 時間: 2025-3-30 00:34 作者: slipped-disk 時間: 2025-3-30 07:23
Ab Initio Molecular Dynamicshe difference between the Car–Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.作者: Meditative 時間: 2025-3-30 10:37 作者: 牢騷 時間: 2025-3-30 15:16
Molecular Docking Methodologiesthe most favorable ligand–target spatial configuration and an estimate of the corresponding complex free energy, although as stated at the beginning accurate scoring methods remain still elusive. In this chapter, the state of art of molecular docking methodologies and their applications in drug discovery is summarized.作者: PLE 時間: 2025-3-30 18:59 作者: 人造 時間: 2025-3-30 23:43 作者: Bridle 時間: 2025-3-31 01:29 作者: Canary 時間: 2025-3-31 07:16 作者: white-matter 時間: 2025-3-31 10:58 作者: grovel 時間: 2025-3-31 13:55
https://doi.org/10.1007/978-0-387-87809-6e field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on larg作者: 沒血色 時間: 2025-3-31 20:45
J. M. Bogoya,S. M. Grudsky,E. A. Maximenkoalgorithms for the integration of Newton’s equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms作者: 抱怨 時間: 2025-4-1 01:28
J. S. E. Feitwell,R. I. Vane-Wrightrge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble perform作者: 開始發(fā)作 時間: 2025-4-1 02:48
https://doi.org/10.1007/978-94-009-8638-1logical macromolecules. We start by summarizing the historical background and then describe classical pairwise additive potential energy functions. We introduce the problem of the calculation of nonbonded interactions, of particular importance for charged macromolecules. Different parameterization p作者: 無思維能力 時間: 2025-4-1 06:40
