Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation [0.03%]
从分子动力学模拟中获得关于固有无序蛋白结合的见解
Christopher M Baker,Robert B Best
Christopher M Baker
Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, wit...
Łukasz Nierzwicki,Pablo Ricardo Arantes,Aakash Saha et al.
Łukasz Nierzwicki et al.
Allostery is a fundamental property of proteins, which regulates biochemical information transfer between spatially distant sites. Here, we report on the critical role of molecular dynamics (MD) simulations in discovering the mechanism of a...
Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling [0.03%]
通过分子建模在实验空间和时间尺度上连接染色质结构和功能
Stephanie Portillo-Ledesma,Tamar Schlick
Stephanie Portillo-Ledesma
Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and comput...
Lucas J Karas,Chia-Hua Wu,Ranjita Das et al.
Lucas J Karas et al.
Hydrogen bonding principles are at the core of supramolecular design. This overview features a discussion relating molecular structure to hydrogen bond strengths, highlighting the following electronic effects on hydrogen bonding: electroneg...
Eran Eyal,Anindita Dutta,Ivet Bahar
Eran Eyal
Recent years have seen a significant increase in the number of computational studies that adopted network models for investigating biomolecular systems dynamics and interactions. In particular, elastic network models have proven useful in e...
David S Cerutti,David A Case
David S Cerutti
The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of w...
Balaji Nagarajan,Nehru Viji Sankaranarayanan,Umesh R Desai
Balaji Nagarajan
Glycosaminoglycans (GAGs) represent a formidable frontier for chemists, biochemists, biologists, medicinal chemists and drug delivery specialists because of massive structural complexity. GAGs are arguably the most complex, natural linear b...
H G Othmer
H G Othmer
Movement requires force transmission to the environment, and motile cells are robustly, though not elegantly, designed nanomachines that often can cope with a variety of environmental conditions by altering the mode of force transmission us...
Computational protein structure refinement: Almost there, yet still so far to go [0.03%]
蛋白质结构计算优化：已经接近目标，但仍任重道远
Michael Feig
Michael Feig
Protein structures are essential in modern biology yet experimental methods are far from being able to catch up with the rapid increase in available genomic data. Computational protein structure prediction methods aim to fill the gap while ...
Sebastian Mai,Philipp Marquetand,Leticia González
Sebastian Mai
We review the Surface Hopping including ARbitrary Couplings (SHARC) approach for excited-state nonadiabatic dynamics simulations. As a generalization of the popular surface hopping method, SHARC allows simulating the full-dimensional dynami...