作者: fatty-streak 時(shí)間: 2025-3-21 21:36 作者: LAPSE 時(shí)間: 2025-3-22 00:35
978-1-4939-9610-0Springer Science+Business Media, LLC, part of Springer Nature 2019作者: 違法事實(shí) 時(shí)間: 2025-3-22 07:34
Massimiliano Bonomi,Carlo CamilloniIncludes cutting-edge methods and protocols.Provides step-by-step detail essential for reproducible results.Contains key notes and implementation advice from the experts作者: 冷淡一切 時(shí)間: 2025-3-22 10:10 作者: 玩笑 時(shí)間: 2025-3-22 16:26 作者: 凹室 時(shí)間: 2025-3-22 18:20 作者: CHAFE 時(shí)間: 2025-3-22 23:06
Data Quality—Lifeblood of Digitalizationuse of the potential pharmaceutical applications. With the continuous advancement of computer technology, it is now possible to study RNA folding. Molecular mechanics calculations are useful in discovering the structural and thermodynamic properties of RNA systems. Yet, the predictions depend on the作者: 頑固 時(shí)間: 2025-3-23 05:08
https://doi.org/10.1007/978-3-662-67782-7ow QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field represe作者: 不可知論 時(shí)間: 2025-3-23 06:50
Fan Wang,Chunhua Deng,Bo Yuan,Chao Chen to four heavy atoms to one CG particle. The effective interactions between the CG particles are parametrized to reproduce partitioning free energies of small chemical compounds between polar and apolar phases. In this chapter, a summary of the key elements of this CG force field is presented, follo作者: Inclement 時(shí)間: 2025-3-23 12:41 作者: SPECT 時(shí)間: 2025-3-23 14:41
https://doi.org/10.1007/978-3-030-33642-4 systems with rugged free-energy landscapes. This method was then applied to the protein-folding problem in combination with molecular dynamics (MD) simulation. Owing to its simplicity and sampling efficiency, the replica-exchange method has been applied to many other biological problems and has bee作者: 哀求 時(shí)間: 2025-3-23 21:40
Leonard F. Koziol,Paul Beljan,Lauren Barkerding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological proces作者: Fabric 時(shí)間: 2025-3-24 01:54 作者: CHASE 時(shí)間: 2025-3-24 04:42 作者: 無(wú)法取消 時(shí)間: 2025-3-24 07:48
https://doi.org/10.1007/978-3-642-34059-8lecular dynamics (MD) simulations. Many sampling schemes rely on adding an external bias to favor the sampling of transitions and to estimate the underlying free energy landscape. Nevertheless, sampling molecular processes described by many order parameters, or collective variables (CVs), such as co作者: 貨物 時(shí)間: 2025-3-24 11:21 作者: HOWL 時(shí)間: 2025-3-24 14:57
https://doi.org/10.1007/978-3-319-07419-1prior knowledge of the system and deals with all sources of uncertainty and errors as well as with system heterogeneity. Furthermore, metainference can be implemented using the metadynamics approach, which enables the computational study of complex biological systems requiring extensive conformation作者: Formidable 時(shí)間: 2025-3-24 19:04
https://doi.org/10.1007/978-3-319-07419-1allenge for experimental methods to determine high-resolution structural models. To meet this challenge, experiments are combined with molecular simulations. The latter propose models for structural ensembles, and the experimental data can be used to steer these simulations and to select ensembles t作者: 殘暴 時(shí)間: 2025-3-25 00:13
https://doi.org/10.1007/978-3-319-07419-1 principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical作者: Epidural-Space 時(shí)間: 2025-3-25 06:22 作者: conduct 時(shí)間: 2025-3-25 08:13
Book 2019sical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; 作者: conifer 時(shí)間: 2025-3-25 12:47 作者: Reservation 時(shí)間: 2025-3-25 18:53 作者: 敬禮 時(shí)間: 2025-3-25 22:09 作者: 調(diào)色板 時(shí)間: 2025-3-26 00:33
Débora B. Maehler,Beatrice Rammstedtthe different analysis algorithms to estimate binding affinity and residence times. We conclude with a survey of published applications that provides explicit examples of successful simulations for several targets.作者: Focus-Words 時(shí)間: 2025-3-26 07:59 作者: Systemic 時(shí)間: 2025-3-26 12:26
Atomistic Force Fields for Proteinsrs for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.作者: 表示向下 時(shí)間: 2025-3-26 16:16
Quantum Chemical and QM/MM Models in Biochemistryodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.作者: 拱形大橋 時(shí)間: 2025-3-26 17:45 作者: Resistance 時(shí)間: 2025-3-26 22:25 作者: 玩笑 時(shí)間: 2025-3-27 02:57
Coevolutionary Analysis of Protein Sequences for Molecular Modelingct prediction through two examples, focusing on the predictions of inter-residue contacts in a single protein domain and on the analysis of a multi-domain protein that undergoes functional, large-scale conformational transitions.作者: Anthology 時(shí)間: 2025-3-27 05:43
1064-3745 ation advice from the expertsThis volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in thi作者: 高調(diào) 時(shí)間: 2025-3-27 12:29 作者: Constituent 時(shí)間: 2025-3-27 14:35
https://doi.org/10.1007/978-3-319-07419-1 learning how to model the structural ensemble of a small disordered peptide by combining state-of-the-art molecular mechanics force fields with nuclear magnetic resonance data, including chemical shifts, scalar couplings and residual dipolar couplings.作者: mediocrity 時(shí)間: 2025-3-27 18:11
Metadynamics to Enhance Sampling in Biomolecular Simulationsduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.作者: Electrolysis 時(shí)間: 2025-3-27 22:34 作者: 萬(wàn)花筒 時(shí)間: 2025-3-28 03:30
1064-3745 -edge and comprehensive, .Biomolecular Simulations: Methods and Protocols. is a valuable resource for both novice and expert researchers who are interested in studying different a978-1-4939-9610-0978-1-4939-9608-7Series ISSN 1064-3745 Series E-ISSN 1940-6029 作者: 猜忌 時(shí)間: 2025-3-28 08:23
Data Quality—Lifeblood of Digitalizationnic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polar作者: 果核 時(shí)間: 2025-3-28 12:25
Data Quality—Lifeblood of Digitalizationeral RNA torsions is briefly described. Applications of the revised torsional parameters to study RNA nucleosides, single-stranded RNA tetramers, and RNA repeat expansions are described in detail. It is concluded that RNA force fields require constant revisions and should be benchmarked against dive作者: Decrepit 時(shí)間: 2025-3-28 18:24 作者: Ceremony 時(shí)間: 2025-3-28 19:31 作者: 憤怒歷史 時(shí)間: 2025-3-29 01:11
Leonard F. Koziol,Paul Beljan,Lauren Barker space, complexity of simulation set up and analysis, and the large computational resources required to pursue such calculations. Over the past few years, there have been advances in computing power, classical force field accuracy, enhanced sampling algorithms, and simulation setup. This has led to 作者: climax 時(shí)間: 2025-3-29 06:33
https://doi.org/10.1007/978-3-642-34059-8e, such a sampling scheme can handle an arbitrarily large number of CVs. A standard enhanced sampling technique combined with an adaptive path-CV can then locate the mean transition pathway and obtain the free energy profile along the path. In this chapter, we discuss the adaptive path-CV formalism 作者: 社團(tuán) 時(shí)間: 2025-3-29 10:49
David Cherney,Yuko Kurauchi,Alex McIntoshar dynamics package GROningen MAchine for Chemical Simulations (GROMACS). The instructions readily transfer to a large variety of other tasks, allowing the reader to use the cloud for their specific purposes..Importantly, by using Docker containers, a popular?light-weight?virtualization solution, an作者: RAFF 時(shí)間: 2025-3-29 14:40 作者: instulate 時(shí)間: 2025-3-29 15:47
https://doi.org/10.1007/978-3-319-07419-1. The computational aspects of this approach are implemented in our open-source . (IMP), a comprehensive and extensible software package for integrative modeling (.). In particular, we rely on the . (PMI) module of IMP that provides facile mixing and matching of macromolecular representations, restr作者: perimenopause 時(shí)間: 2025-3-29 20:47 作者: Obliterate 時(shí)間: 2025-3-30 00:48
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Fielderal RNA torsions is briefly described. Applications of the revised torsional parameters to study RNA nucleosides, single-stranded RNA tetramers, and RNA repeat expansions are described in detail. It is concluded that RNA force fields require constant revisions and should be benchmarked against dive作者: DAUNT 時(shí)間: 2025-3-30 07:12 作者: 賞錢(qián) 時(shí)間: 2025-3-30 09:33 作者: 苦澀 時(shí)間: 2025-3-30 12:54
Protein–Ligand Binding Free Energy Calculations with FEP+ space, complexity of simulation set up and analysis, and the large computational resources required to pursue such calculations. Over the past few years, there have been advances in computing power, classical force field accuracy, enhanced sampling algorithms, and simulation setup. This has led to 作者: 無(wú)瑕疵 時(shí)間: 2025-3-30 18:37 作者: 增強(qiáng) 時(shí)間: 2025-3-31 00:23 作者: cluster 時(shí)間: 2025-3-31 02:36
Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropd to integrative structural modeling. We also briefly sketch the “minimum ensemble method,” a maximum-parsimony refinement method that seeks to represent an ensemble with a minimal number of representative structures.作者: 可卡 時(shí)間: 2025-3-31 08:45 作者: fertilizer 時(shí)間: 2025-3-31 09:52 作者: engrossed 時(shí)間: 2025-3-31 15:42
Atomistic Force Fields for Proteins, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some?biologically relevant time scales?(microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad 作者: orient 時(shí)間: 2025-3-31 20:13
Force Fields for Small Molecules such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also a作者: Alveoli 時(shí)間: 2025-4-1 01:05
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Fielduse of the potential pharmaceutical applications. With the continuous advancement of computer technology, it is now possible to study RNA folding. Molecular mechanics calculations are useful in discovering the structural and thermodynamic properties of RNA systems. Yet, the predictions depend on the作者: Obituary 時(shí)間: 2025-4-1 02:26
